key: cord-349624-2sypsfba authors: ferigato, sabrina; fernandez, michelle; amorim, melania; ambrogi, ilana; fernandes, luísa m m; pacheco, rafaela title: the brazilian government's mistakes in responding to the covid-19 pandemic date: 2020-10-20 journal: lancet doi: 10.1016/s0140-6736(20)32164-4 sha: doc_id: 349624 cord_uid: 2sypsfba nan submissions should be made via our electronic submission system at http://ees.elsevier.com/ thelancet/ www.thelancet.com published online october 20, 2020 https://doi.org/10.1016/s0140-6736(20)321644 1 the brazilian government's mistakes in responding to the covid-19 pandemic it is unfortunate to read the unsub stantiated and misguided opinion of a few physicians about the role of the current administration during the covid19 crisis in brazil. 1 for those of the international scien tific community who base their understanding on reliable data, the conclusion that brazil has shown one of the worst responses to the pan demic is unequivocal. 2 the gravity of the pandemic in brazil is evidenced by the current epidemiological facts: brazil is among the three countries with the largest number of confirmed cases (more than 5 million as of oct 15, 2020, according to who), with high mortality, 3 evidence of underreporting, 3 and a high number of deaths among health professionals, pregnant women, 4 and the indigenous population. the federal government's denial of science and, consequently, of the seriousness of the pandemic to the health and wellbeing of brazilians has led to a failure to coordinate, promote, and finance internationally sanctioned public health measures. the ministry of health has not developed a national plan to combat the pandemic, 3 nor has any other federal government agency. states and municipalities continue to be neglected and receive insufficient assistance. influenced by political interests, the federal government has disrupted the flow of financial transfers and slowed the deliveries of essential supplies to certain regions. furthermore, brazil's public health system, sistema único de saude (sus), is the largest in the world and provides universal coverage without any cost to patients. it is accessible nationwide and provides communitybased primary health care to more than 70% of the population. yet, primary health care has been overlooked by the federal government as a key element in this public health crisis response. financial emergency aid to the most vulnerable populations was gravely delayed, insufficient, and cumbersome to obtain. moreover, the federal administration denies international recommendations for nonpharmacological interventions, refusing to establish a national man date for social isolation and mask use. it is necessary to analyse the brazilian government's response to the covid19 pandemic based on trustworthy knowledge built upon scientific facts. the negative effects of governmental decisions represent important risks to the health of brazilians and for the pandemic's global situation. a coordinated politi cal response guided by social justice and evidencebased knowledge is essential to managing any public health emergency, especially one with as broad economic and health impacts as covid19. regretfully, this is not what is happening in brazil. we declare no competing interests. brazil's covid19 response lancet covid19 commission statement on the occasion of the 75th session of the un general assembly covid19: public policies and society's responses. quality information for refining public policies and saving lives the tragedy of covid19 in brazil: 124 maternal deaths and counting for more on covid-19 in brazil's indigenous population see key: cord-300795-s7y9m8iu authors: brandão, paulo e.; ayres, giselle r. r.; torres, carolina a.; villarreal, laura y. b.; hora, aline s.; taniwaki, sueli a. title: complete genome sequence of a brazil-type avian coronavirus detected in a chicken date: 2016-10-13 journal: genome announc doi: 10.1128/genomea.01135-16 sha: doc_id: 300795 cord_uid: s7y9m8iu avian coronavirus is the causative agent of infectious bronchitis in chickens, leading to multisystemic disease that might be controlled if adequate vaccine strains are used. this paper reports the first complete genome sequence of a brazil type of this virus (27,615 nucleotides [nt]) isolated from the kidneys of a chicken. navirinae:gammacoronavirus) host-type avian infectious bronchitis virus (ibv) in chickens occurs as multiple types grouped in six genotypes, with a total of 32 lineages based on spike s gene comparisons, and it is involved in multisystem highly contagious infections of chickens (1, 2) . the positive-sense, singlestranded, 5=-capped genomic rna (ca. 27 kb) codes for the replicase complex (open reading frame 1 [orf1]) and five structural proteins on the remaining 1/3 at the 3= end: spike s, envelope protein e, membrane protein n, and nucleocapsid protein n, besides the accessory proteins 3a, 3b, 5a, and 5b, with an untranslated region (utr) at both the 5= and 3= ends (3, 4) . although a typical brazilian type of ibv has been reported (5), no complete genome sequence was available hitherto for this type. the gammacoronavirus/avcov/chicken/brazil/23/2013 ibv strain was isolated after three serial passages in 11-day-old chicken embryonated eggs from the kidneys of a chicken from brazil collected in 2013. random double-stranded cdnas were obtained from clarified (12,000 ϫ g/15 min/4°c), filtered (0.45-m-poresize), and dnase/rnase-treated allantoic fluid using superscript iii and klenow exo-dna polymerase (life technologies) after total rna extraction with trizol reagent (life technologies) and rneasy minikit (qiagen). libraries and sequencing kits were by illumina (nextera xt index, nextera xt dna), and reads were obtained with a nextseq 500 (illumina) using the nextseq500 mid output version 2 kit (150 cycles). the consensus sequence was assembled with clc genomics workbench version 8.5.1 (qiagen), using avcov sequence with accession number kj425485.1 as a reference and with reads that were trimmed for quality (limit, 0.05). a total of 10,274,194 paired-end reads were obtained, and from this, 7,558,298 reads were mapped. the resulting genome was 27,615 nucleotides (nt) long, including the poly(a) tail, and is organized as 5= utr (nt 1 to 528), orf1a (nt 529 to 12318), and orf1ab (nt 12318 to 20357), with a ribosomal frameshift between these two orfs, followed by the genes spike s (nt 20308 to 23817), 3a (nt 23817 to 23990), 3b (23990 to 24181), envelope e (nt 24165 to 24488), membrane m (nt 24457 to 25137), 5a (nt 25497 to 25694), 5b (nt 25691 to 25939) and nucleocapsid n (25882 to 27111), with a 3= utr at nt 27112 to 27615, including the poly(a) tail. spike sequence-based analysis revealed that strain gammacoronavirus/avcov/chicken/brazil/23/2013 belongs to the gi-11 avcov lineage (brazil type) with only 82.9% nt identity with the massachusetts (gi-1) type used as a live vaccine in brazil against avian infectious bronchitis; this low identity is one of the reasons for the lower protection given by this vaccine reported after challenges with the brazil type (6). this full genome of a brazil type ibv will now allow for improved analyses on the origins of this lineage and a better association with vaccine protection studies. accession number(s). the gammacoronavirus/avcov/chicken/brazil/23/2013 complete genome sequence is deposited in genbank under the accession number kx258195. this work, including the efforts of paulo eduardo brandão, was funded by mcti | conselho nacional de desenvolvimento científico e tecnológico (cnpq) (301225/2013-3). this work, including the efforts of paulo eduardo brandão, giselle razzera rosso ayres, carolina alejo torres, and aline s. hora, was funded by fundação de amparo à pesquisa do estado de são paulo (fapesp) (2015/ 17889-6). review of infectious bronchitis virus around the world s1 gene-based phylogeny of infectious bronchitis virus: an attempt to harmonize virus classification molecular evolution and emergence of avian gammacoronaviruses coronavirus avian infectious bronchitis virus molecular epidemiology of avian infectious bronchitis in brazil from 2007 to 2008 in breeders, broilers, and layers increased level of protection of respiratory tract and kidney by combining different infectious bronchitis virus vaccines against challenge with nephropathogenic brazilian genotype subcluster 4 strains key: cord-307306-ju0vcalk authors: barbosa, daniel a. n.; de oliveira-souza, ricardo; gorgulho, alessandra; de salles, antonio title: upholding scientific duty amidst poisonous disinformation date: 2020-07-22 journal: cureus doi: 10.7759/cureus.9339 sha: doc_id: 307306 cord_uid: ju0vcalk because of a recent politically-biased lancet editorial, the world’s opinion has been directed against the brazilian government over the rising numbers of covid-19 cases in the country. this is an example of reporting data without accounting for important covariates. epidemiological figures should always be corrected for population size. in fact, brazil is not even on the list of the 10 countries with the highest number of deaths per 100,000 people. belgium, the united kingdom, and spain are the most affected countries in this regard. the disinformation presented by a renowned medical journal has ignited severe criticisms against a chief-of-state for not promoting a generalized lockdown in a country of continental size. as scientists, we have a duty to stress the caveats of science instead of fueling political attacks, and we should refrain from jumping to uninformed conclusions without considering well-analyzed data. moreover, while there is no evidence to endorse the efficacy of a generalized lockdown in socioeconomically vulnerable populations, it is undoubtedly associated with severe nationwide adverse effects. in a recent lancet editorial, the world's attention was directed toward the rising numbers of confirmed covid-19 cases and deaths in brazil [1] . it highlighted some worrisome projections from studies by the imperial college, london [1] . during the current global health crisis, articles in renowned medical journals have guided public policies and investments in healthcare [2] . consequently, scientific information has gained the power to alleviate the suffering of societies; however, disinformation, on the other hand, causes suffering and ruins livelihoods [3] . brazil is now the country with the second-highest total number of confirmed covid-19 cases and deaths [4] . yet, as scientists, we cannot interpret this piece of raw data without accounting for covariates. brazil has the sixth largest population in the world; therefore, this raw number must be corrected by its population size. it turns out that brazil has never been among the 10 large countries with the highest number of deaths per 100,000 people. that list is headed by belgium, the united kingdom, and spain [4]. as of july 12, 2020, brazil occupies the 12th spot in that list ( table 1) . such a spurious manner of reporting public health data is completely unacceptable even by the lay media, let alone by a renowned scientific journal [1,2,4]. the lancet focused on politics instead of a scientific analysis of the pandemic's status in brazil, an odd choice for a scientific publication. data not corrected for population size was used to build the claim that "perhaps the biggest threat to brazil's covid-19 response is its president ", and that "brazil's leadership has lost its moral compass, if it ever had one" [1] . the editorial failed to provide scientific support, but rather echoed politically-biased ideas. the lancet's manifesto is merely a science-fueled attack against a chief-of-state for advising state governors to reopen the economy, and serves instead to encourage a policy of generalized lockdown, which is associated with severe nationwide adverse effects, i.e., increased poverty, conjugal crises, street criminality, depression, suicide, and substance abuse. calling the lockdown a "sensible measure" contrasts with fair criticisms against leaders embracing policies without sufficient evidence of their efficacy and safety. in fact, the universal lockdown adopted by brazilian mayors and state governors has not slowed down the growing raw number of covid-19 cases; instead, it has proven to be extremely harmful to several underserved communities [5] . indeed, physical distancing and hygiene recommendations are impossible to follow in brazil's underserved communities, as pointed out by the same editorial [1] . the forceful implementation of these measures has oppressed vulnerable populations, by instilling hunger and crime [5] . it is irresponsible to use poorly analyzed data to accuse leaders, countries, and doctors working with the best of intentions to fight a pandemic that has caused immense misery even in the most developed countries. the use of disinformation to point fingers against those fighting in extremely difficult conditions against the same misery, covid-19, for the benefit of their underserved people is inhuman and unfair, and the heroes of this pandemic deserve better. the lancet's editorial board should at least publish a note apologizing for these unfounded accusations and lack of sensibility [1, 2, 4 ]. while we seek to serve the people with a scientific outlook and approaches, a pertinent question arises: when are our colleagues in the medical field going to stop delivering politically-biased disinformation? editorial (anonymous): covid-19 in brazil covid-19: brazil now has third highest number of cases behind us and russia disinformation: former spy chief reveals secret strategies for undermining freedom, attacking religion, and promoting terrorism lockdown puts brazilian lives at risk in compliance with the icmje uniform disclosure form, all authors declare the following: payment/services info: all authors have declared that no financial support was received from any organization for the submitted work. financial relationships: all authors have declared that they have no financial relationships at present or within the previous three years with any organizations that might have an interest in the submitted work. other relationships: all authors have declared that there are no other relationships or activities that could appear to have influenced the submitted work. key: cord-035347-adzkwzz2 authors: quintans-júnior, lucindo josé; albuquerque, george rego; oliveira, sérgio campello; silva, robério rodrigues title: brazil’s research budget: endless setbacks date: 2020-09-21 journal: excli j doi: 10.17179/excli2020-2887 sha: doc_id: 35347 cord_uid: adzkwzz2 nan the budget cuts in science and technology areas in brazil are making the situation untenable for researchers. there is a lack of money to maintain even basic services, and labs are shutting down. the proposed 2021 draft budget would result in a 29 % reduction in science funding since 2015. if this funding cut is not reversed, it will severely damage the current system of scholarships and research. these endless cuts in science funding need to be reviewed by brazilian government and the national congress, or brazilian science will be doomed to continued destruction and dismay for researchers. the crisis in education in brazil is not a crisis; it is a project', this well-known phrase by the renowned brazilian anthropologist and writer, darcy ribeiro (1922 ribeiro ( -1997 (santos and sampaio, 2017) , now also holds true for the area of science. although there have been cuts in funding under previous governments, the cuts proposed by the current bolsonaro government are based on an anti-science ideology. the panaceas and miracle cures proposed by the current government for covid-19 have been yet another embarrassing episode, throwing science into the gutter, and illustrating the current prevalence of a pandemic of ignorance and anti-science attitudes -further exemplified by the disrespect shown to doctors, frontline health workers and family of patients who have died because of the covid-19 outbreak (quintans-júnior and silva, 2020). recently, the brazilian government presented its draft 2021 budget bill (ploa) to congress, which includes proposals for science funding for 2021. despite the science budget on the face of it having a small increase when compared to 2020, in respect of the two main agencies responsible for university and higher education funding in brazil, capes and cnpq, there is a proposed reduction of almost 4 %. a closer analysis of the data reveals a 29 % budget reduction for universities and higher education between 2015 and 2021 (r$ 13.5 billion to r $ 9.6 billion) (ploa, 2021; angelo, 2017) and an unacceptable 41 % cut in research funding from 2015 to 2019. figure 1 shows a clear gap between forecast budgets and what was actually spent on funding brazilian science, all against a background of the demagogic rhetoric of populism of the current government (2020 consider the 2015-2019 average execution of forecasting). one of the most concerning points illustrated by the figure is in relation to fndct funding (ploa, 2021; angelo, 2017) . this was a fund created to finance brazilian science and innovation, but the data clearly shows any increasing gap between the funds theoretically available (budget), and those actually spent (executed) on projects for the development of science in brazil. these data reinforce the idea that the fndct was a project designed solely to disrupt current funding structures and discourage research workers. the gap between the budget and actual spending is on track to be wider than ever in 2020. the situation is made even worse by the depreciation of the brazilian currency, the real, against the us dollar, with its value falling almost 60 % from 2015 to 2020 (trading economics, 2020), so this makes things worse because a lot of research depends on equipment and materials bought from abroad (particularly the usa and europe). the situation in brazil has become so desperate that scientists, as physicist luiz davidovich, has said 'an atomic bomb strike on brazilian science' (angelo, 2017) . the covid-19 outbreak should have emphasized the importance of science and technology in the search to understand the disease, and develop new treatments and vaccines, but in brazil, the atmosphere of scientific denial defended by bolsonaro and his supporters has created a surreal situation, and a complete lack of strategic vision: brazil has been without a minister of health for the last 110 days, having an interim minister (an army general with no medical experience) during the worst pandemic in the last 100 years. the 2021 draft budget also contains an inexplicable (given that fact that brazil is in the middle of a major health crisis) proposed reduction of around 22 % (ploa, 2021) to the health budget, cuts that will not only undermine essential health services, but also mean that important clinical research will have to be stopped. the dramatic reduction in funding over recent years has already produced deleterious effects, with the number of research papers published declining, reflecting the fact that laboratories are reducing their activities. the number of doctors being trained, and the numbers of master's students are also falling, and a brain drain is accelerating because leading researchers are finding it impossible to continue their work in brazil (scalzaretto, 2020) . the brazilian congress should urgently reconsider these proposed budget cuts, review this destructive policy, and impose conditions on the government that ensure that science and higher education in brazil receive appropriate funding, if they do not, a scorched earth scenario will be seen in a short time in relation to science in brazil. brazilian scientists reeling as federal funds slashed by nearly half reply: from chloroquine to anal ozone: how ignorance has helped to kill more than 100,000 brazilians by covid-19 crise social das instituições de ensino superior e a formação em saúde para o mercado. saúde debate this is how economic struggles force brazil's brain drain. the brazilian report the authors declare no conflict of interest. key: cord-252345-06jdg26s authors: carvalho, vitor oliveira; conceição, lino sergio rocha; gois, miburge bolivar title: covid‐19 pandemic: beyond medical education in brazil date: 2020-06-12 journal: j card surg doi: 10.1111/jocs.14646 sha: doc_id: 252345 cord_uid: 06jdg26s nan rethought. 1 the current pandemic has also brought new challenges to medical education in general (eg, physicians, nurses, physical therapists, and pharmaceuticals). as the global emergency grows the need for well-trained staff becomes one of the main focus of universities, hospitals, and government. 2 unfortunately, in emerging countries, there are more challenges to face to educate these professionals in this unprecedented adverse scenario. 3 in brazil, a developing country, the public healthcare system is known to work almost at the maximum of its capacity, which makes the population fear the tragic consequences of covid-19 pandemic. the majority of healthcare education (internships and residency programs) in brazil is still located at public services. online education and the wide use of high technology is not a reality in our educational environment. it seems that our traditional medical education does not follow the new generation's language and way of leaning. during an exponential increase in covid-19 in brazil, a change in our education system is necessary to minimize the possible staff deficit and to avoid massive contamination of students. 4 moreover, online education could be very helpful to enhance experiences and information between hospitals/universities in this very large and unequal country. improving knowledge exchange and avoiding contamination makes perfect sense in the covid-19 pandemic. however, online education requires an important investment in structure and human resources. 5, 6 in a recent article, newman and lattouf brilliantly showed the concern about medical education during the covid-19 pandemic and the necessity of adaptation through technological innovation. however, in a developing country, like brazil, this scenario is more challenging. brazil continuous to face an important educational deficiency. historically, public high-quality education, in general, has not been taken as a high priority. during this pandemic, we notice that priit is time to rethink and modernize our public education system and guarantee equal educational access to our socially vulnerable students. the temporary suspension of academic activities and the lack of use of modern educational tools can be very harmful to a developing country struggling with covid-19. this pandemic is showing how fragile our public educational policies have historically been. in this scenario, we see the brazilian population keep asking themselves three major questions: can we handle this pandemic and its consequences? what are we learning from this pandemic to improve our educational system and public health? can we handle future outbreaks in a globalized world? mental health during and after the covid-19 emergency in italy being a doctor will never be the same after the covid-19 pandemic online ahead of print covid 2019 outbreak: the disappointment in indian teachers medical student education in the time of covid-19 the inevitable reimagining of medical education coalition for medical education-a call to action: a proposition to adapt clinical medical education to meet the needs of students and other healthcare learners during covid-19 key: cord-341212-dk6ioi15 authors: ribeiro, andre luis ribeiro; sousa, naama waléria alves; carvalho, vitor oliveira title: besides the climate model, other variables driving the covid-19 spread in brazil() date: 2020-06-15 journal: sci total environ doi: 10.1016/j.scitotenv.2020.140211 sha: doc_id: 341212 cord_uid: dk6ioi15 nan we have read with great interest the study by auler et al. (auler et al., 2020) , about the influence of climate on covid-19 spread. the authors considered data from the five most affected cities by the current pandemic in brazil. the authors used meteorological data from 13 th of march to 17 th of april 2020 and analyzed weather conditions such as temperature, relative humidity and rainfall against variables like number of cumulative cases, new daily cases and contamination rate to build their study model. the study model and data analysis are well-performed, and although the authors found that temperature and relativity humidity influenced the covid-19 dissemination, other well-known and important variables, such as social distancing, population testing, hand wash (giordano et al., 2020) and rational use of face mask were not part of their study model (feng et al., 2020) . brazil is a continental country with large disparity between cities and regions, with massive differences from socioeconomic to human development. on the other hand, the governors of the state of rio de janeiro and são paulo, among others, are reinforcing social distancing in their state (wikipedia, 2020b) . this dispute was taken to the supreme court, which reinforced the authority of cities and states to define local measures of social distancing, quarantine, prohibition of activities and definition of essential services (federal, 2020) . the covid-19 pandemic started in wuhan, china and spread worldwide. the cities of são paulo and rio de janeiro were the 2 first cities to report cases in brazil, which is possibly explained by their importance in commercial aviation, responsible for almost 80% of the weekly international seats of the country, 62.27% and 17.1% respectively (based on data from november 2019 of the national civil aviation agency of brazil -anac) (regis, 2020) . since the cases started to spread in these cities, uncoordinated measures of social distancing were gradually implemented across the country, in despite of the divergences between the president and governors (wikipedia, 2020a) , (wikipedia, 2020b) . brasilia showed the first case in 7 th march and its history of the pandemic was marked by the trip of the brazilian president to usa between 7 to 10 of march, where evidence that high temperatures and intermediate relative humidity might favor the spread of covid-19 in tropical climate: a case study for the most affected brazilian cities medida cautelar na ação direta de inconstitucionalidade 6.341 distrito federal. supremo tribunal federal rational use of face masks in the covid-19 pandemic modelling the covid-19 epidemic and implementation of population-wide interventions in italy as bolsonaro flouts warnings, coronavirus spreads in brazil seis em cada dez voos internacionais no brasil decolam de sp key: cord-355049-mf0lgrlp authors: martins-filho, paulo ricardo; santos, victor santana title: no evidence supports the use of ether and chloroform inhalation for treating covid-19 date: 2020-03-24 journal: rev panam salud publica doi: 10.26633/rpsp.2020.41 sha: doc_id: 355049 cord_uid: mf0lgrlp nan dear editor, sars-cov-2 has been spreading rapidly across the world as well as the number of fake news on social media regarding harmful or non-harmful treatments which are ineffective for treating covid-19. in brazil, the first case of covid-19 was confirmed on february 26, 2020 and until march 20, 2020 at least 970 cases and seven deaths have been reported. the fear and uncertainty have led people to consume and share mistrust and misinformation on the internet. since the first confirmed case in brazil, fake news about the effectiveness of an ether and chloroform blend known as "lança perfume" or "loló" were spread on social media. nowadays, the ecosystem of big data has provided valuable information about online health-related behaviour and new patterns among population groups using social media data. google trends may act as an efficient real time surveillance system by monitoring hit searches of specific health issues leading to reliable and meaningful indicators to track health information demand and supply trends (1). we used google trends to assess recent search activity (from february 25 to march 20, 2020) on the novel coronavirus in brazil and the popularity of related search terms. related searches for coronavirus revealed a high level of interest (a breakout over 5000%) on the information about the use of an ether and chloroform blend in treating covid-19, especially in the north and northeast regions which are recognized as the poorest regions in the country. the use of internet as a source of health information has increased over the years, but reporting incomplete aspects of scientific studies, misinterpreting the findings and highlighting unusual claims have become common practice. unfortunately, fake news and misinformation on social media can lead people to make harmful health decisions. it is important to check health information related to covid-19 from reliable news sources and expert guidance from health authorities and international health organizations, rather than from shared stories in social media. journalists and health-care professionals should cooperate with an effective communication to enhance healthy attitudes towards the pandemic (2) . although the epidemic use of the ether and chloroform as a recreational drug in brazil has been generally neglected in the world literature of public health (3) and quantitative data of human fatality after acute inhalation exposure to this drug combination are not available, there is evidence from human and animal studies that chloroform may lead to hepatic, renal and cardiovascular injury (4-6). furthermore, there is no evidence supporting claims that ether and chloroform inhalation is useful in the treatment of covid-19. authorities should reinforce the need to seek information from government agencies and national and international health organizations. a google trends-based approach for monitoring nssi 2019-ncov, fake news, and racism social rank and inhalant drug use: the case of lança perfume use in são paulo, brazil. drug alcohol depend mechanisms involved in cardiac sensitization by volatile anesthetics: general applicability to halogenated hydrocarbons? experimentation" with chloroform key: cord-350859-0khu9mz3 authors: grotto, rejane maria tommasini; santos lima, rodrigo; de almeida, gabriel berg; ferreira, claudia pio; guimarães, raul borges; pronunciate, micheli; azevedo, edmur; catão, rafael de castro; fortaleza, carlos magno castelo branco title: increasing molecular diagnostic capacity and covid-19 incidence in brazil date: 2020-08-18 journal: epidemiology and infection doi: 10.1017/s0950268820001818 sha: doc_id: 350859 cord_uid: 0khu9mz3 different countries have adopted strategies for the early detection of sars-cov-2 since the declaration of community transmission by the world health organization (who) and timely diagnosis has been considered one of the major obstacles for surveillance and healthcare. here, we report the increase of the number of laboratories to covid-19 diagnosis in brazil. our results demonstrate an increase and decentralisation of certified laboratories, which does not match the much higher increase in the number of covid-19 cases. also, it becomes clear that laboratories are irregularly distributed over the country, with a concentration in the most developed state, são paulo. different countries have adopted strategies for the early detection of sars-cov-2 since the declaration of community transmission of the virus by the world health organization (who), allowing early clinical intervention and the management of these patients with nonpharmacological measures such as hospital isolation, suspension of regular activities and respiratory support in intensive care units (icus) promptly after diagnosis [1] . timely diagnosis has been considered one of the major obstacles for surveillance and healthcare (especially hospital) preparedness in low-to-middle income countries [2] . with that in mind, we studied the increase in covid-19 molecular diagnostic capacity of public health laboratories in different regions in brazil. we were especially interested in analysing the association of newly certified laboratories with the increase of covid-19. therefore, we searched the epidemiological bulletins provided by the ministry of health of brazil (available at https://covid.saude.gov.br/) for the weekly incidence of laboratoryconfirmed cases; and the union official diary (a daily publication of the federal government official decrees, available at https://www.jusbrasil.com.br/diarios/dou/) to identify new certifications of public laboratories for the molecular diagnosis of sars-cov-2. our analysis was carried out until 4th june, when the introduction of sars-cov-2 in the country completed 100 days. both the number of newly certified laboratories and the weekly incidence of laboratory-confirmed covid-19 were submitted to joinpoint regression, using software joinpoint 4.8 (national cancer institute, calverton, md) [3] . this analysis detects changes in rate trends, and was performed using a log link function to fit the data. we also performed univariate and single-step multivariable poisson regression model, with the number of laboratories and the epidemiological weeks as predictors for the outcome of interest (rate of covid-19 confirmed cases), using stata 14 (statacorp, college station, tx), and georeferenced the time of introduction of covid-19 and certification of laboratories in different areas in brazil, using arcgis 10 (esri, redlands, ca). we then applied the inverse distance weighted (idw) technique to interpolate discrete cases and transform it in a continuous surface in raster format, highlighting the date of case arrival and the geographic region. idw is a local deterministic interpolator which does not exceed data intervals between neighbours. we used 20 neighbours and a 1.5 power factor. the diffusion layer was overlaid with the laboratories mapped by municipality and week of certification. our results are shown in figure 1 . we can observe on the map (panel c) the covid-19 spatial diffusion pattern, starting in the main metropolis throughout the country, mainly são paulo, rio de janeiro, fortaleza, recife and manaus. the diffusion follows the path of the urban network going from major metropolis to middle size cities and then to small cities. the velocity of the spread is different among the regions of the country. in north of brazil, the diffusion was extremely fast despite lack of road transport in several portions. in northeast and southeast regions, metropolitan areas and cities with higher populational density concentrated the early cases of covid-19, spreading after towards the interior of each region. in south and midwest regions, the diffusion was at the initial stages, centred in major urban areas and near major road axis. panel a shows the rate of certifications of public laboratories for the molecular diagnosis of sars-cov-2 by epidemiological week, whereas panel b shows the rate of incidence of laboratoryconfirmed covid-19 by epidemiological week, both in a joinpoint regression analysis (per 100 000 inhabitants). one can note an increase of certified laboratories, which does not match the much higher increase in the number of cases. the laboratory's certification ranged from few laboratories (one in the north-northeast region, one in the middle east and south and two in southeast) to 26 labs, in 8 weeks. almost all regional centres of the country certificated at least one laboratory. in summary, at week 23 the ratio between the number of laboratories to population density (population per km 2 at the last census at 2010) at each brazil's region was 6:4.14, 4:8.75, 28:86.92, 3:48.58 and 7:34.15, respectively, at north, middle east, southeast, south and northeast. it is also clear from panel c that laboratories are irregularly distributed over the country, with a concentration in the most developed state, são paulo (13 of 35 laboratories). however, a decentralisation trend can be seen over the last epidemiological weeks, highlighted by the presence of newly certified laboratories specially in north and northern regions of brazil. it is important to reveal that in são paulo state there are many cities performing mass testing, and this could explain the greater growth in the number of labs. interestingly, the number of laboratories is positively associated with the number of covid-19 cases in the univariate model (incidence rate ratio (irr), 1.11; 95% confidence interval (ci), 1.11-1.11) but negatively associated after adjusting for epidemiological week (number of laboratories: irr, 0.98; 95% ci 0.97-0.99; epidemiological week: irr, 1.70; 95% ci 1.69-1.71). this finding can be interpreted in two directions. from an optimistic perspective, the slow increase in certifications of new laboratories for diagnosis does not necessarily correlates with the overall diagnostic capacity of the laboratory net, once already certified individual laboratories may increase their own capacity as well. this analysis could not be performed as no data were available regarding diagnostic capacity of each one of these laboratories. from a pessimistic perspective, the fast increase of covid-19 incidence and the continuous spread into inner country, less developed areas of brazil challenges diagnostic fig. 1 . trends on sars-cov-2 infection and laboratory capacity in brazil over one hundred days since first covid-19 confirmed case. section a shows the rate of certifications of public laboratories for the molecular diagnosis of sars-cov-2 by epidemiological week, in a joinpoint regression analyzes. section b shows the rate of incidence of laboratory-confirmed cases by epidemiological week, also in a joinpoint regression analyzes. section c shows temporal-spatial diffusion of covid-19 in brazil: warm colors designate early introduction (i.e. 12-14 epidemiological weeks), while cool colors designate recent introduction (i.e. 19-20 epidemiological week). certified laboratories for sars-cov-2 infection molecular diagnosis are represented by squares in greyscale also in section c. the shades of grey range from the darkest for the three initial certified public health laboratories to the light grey representing those that were certified in later stages of the outbreak. capacity and therefore, accurate and timely health surveillance [4] . this implies that, given the fast increase of covid-19 cases and the continuous spread into inner brazil [5] , the laboratories (which are continuously increasing their capacity) may still be insufficient to provide accurate data in a setting of exhaustion of hospital (especially icus) capacity [6] . the primacy of the growth of cases over laboratory capacity is reinforced by the increase in hospital admissions and deaths (as reported in official data (https://covid.saude.gov.br/) and recent studies [7, 8] ). health surveillance has been a strong pillar of response to previous public health emergencies in brazil, including pandemic h1n1 influenza and zika virus [9] . challenges for covid-19 response are not restricted to health surveillance [10] , but strengthening an accurate knowledge of its behaviour can direct preventive strategies (including infection control). serial antibody prevalence surveys may be an option but are still hampered by inaccurate serological tests [11] . given that quarantine measures started to be relaxed in national territory, this is a critical moment where diagnosis missing can jeopardise the epidemic control. therefore, brazilian states must increase their capacity of timely molecular diagnosis, not only to face this pandemic, but as a network for preparedness for future public health emergencies [12] . effects of non-pharmaceutical interventions on covid-19 cases, deaths, and demand for hospital services in the uk: a modelling study electronic health information systems to improve disease diagnosis and management at point-of-care in low and middle income countries: a narrative review permutation tests for joinpoint regression with applications to cancer rates the covid-19 pandemic in brazil: chronicle of a health crisis foretold taking the inner route: spatial and demographic factors affecting vulnerability to covid-19 among 604 cities from inner são paulo state risk of the brazilian health care system over 5572 municipalities to exceed health care capacity due to the 2019 novel coronavirus (covid-19) covid-19 epidemic in brazil: where are we at covid-19: intensive care units, mechanical ventilators, and latent mortality profiles associated with case-fatality in brazil. cadernos de saúde pública covid-19 in brazil: advantages of a socialized unified health system and preparation to contain cases the lancet (2020) covid-19 in brazil: 'so what?'. lancet remarkable variability in sars-cov-2 antibodies across brazilian regions: nationwide serological household survey in 27 states. medrxiv 2020.05.30 a public health laboratory response to the covid-19 pandemic grotto and fortaleza: concept and design the study and drafting of the manuscript; lima, de almeida and pronunciate: acquisition of date; ferreira, guimarães, catao and pugliesi: analysis and interpretation of date; all authors: critical revision of the manuscript for important intellectual content. data availability statement. the authors state that the database used in the analyses can be available as a supplementary file to the paper or provided to interested researchers upon reasonable request. key: cord-307089-344rhiw0 authors: marson, fernando augusto lima; ortega, manoela marques title: covid-19 in brazil date: 2020-04-27 journal: pulmonology doi: 10.1016/j.pulmoe.2020.04.008 sha: doc_id: 307089 cord_uid: 344rhiw0 nan it has been ~4 months since the first case of coronavirus disease 2019 (covid-19) was reported in wuhan, china including a total of ~82,000 patients and 3,341 deaths. until april 14 th , 2020, covid-19 has affected ~1,950,000 patients in 210 countries and territories around the world and 2 international conveyances and caused ~122,000 deaths in 162 countries/territories 1 . however, the epidemiologic data differs across countries. although china showed the first case and a higher rate of morbidity and mortality than other sites, the number of new cases per day in china has been less than that elsewhere since february 26, 2020. further studies and continued monitoring are needed to better understand the underlying mechanism of covid-19. in addition, united states of america (usa) exceeded the number of cases observed in china on march 28 th , 2020 with more than 590,000 covid-19 patients and ~24,000 deaths, followed by spain (~172,000 patients and ~18,000 deaths), italy (~160,000 patients and ~20,000 deaths), france (~137,000 patients and ~15,000 deaths), germany (~130,000 patients and ~3,000 deaths), united kingdom (~94,000 patients and ~12,000 deaths) and iran (~75,000 patients and ~4,700 deaths) by april 14 th , 2020. several effective measures including restricting travel from china, controlling the distribution of masks, extensive research of covid-19 spread, and government efforts to inform and educate the public were aggressively conducted in taiwan 2 . this is probably the reason why there were only 39 cases (until february 29 th , 2020) with a daily cumulative index of one case per day in taiwan, which was much lower than that of nearby countries, such as republic of korea and japan 2 . in brazil, the number of covid-19 cases is increasing daily and by april 14 th , 2020, 23,955 positive cases have emerged. the number of deaths has also increased to 1,361 covid-19 patients in the country so far. deaths are mainly located in são paulo, which is the most populated state in brazil. china has managed to greatly reduce the virus transmission mostly with three effective measures italy has different demographics and social behavior than china and other countries like germany that coped with the higher ratio of infection and it exceeded the capacity of the health system. italy showed a lower testing capacity than china and other countries such as germany during the first weeks of covid-19 pandemic, but the capacity to perform real-time pcr has improved, giving better epidemiologic data of less severe cases and asymptomatic individuals carrying the coronavirus in the population. however, as a final scenario, usa has shown the highest number of deaths related with covid-19. in brazil, until april 14 th , 2020, the mortality rate was 1,361/23,955 (5.68%). italy was the first country to reach the mark of ten thousand covid-19 related deaths as described by boccia et al. (2020) , which showed a 11.90% of mortality (13,155/110,574). as discussed by the authors, some conditions are closely related to the italian situation such as the size of the aged population (23.1% of citizens from italy versus 13.5% in brazil), the presence of concomitant serious diseases such as chronic obstructive pulmonary disease, ischemic heart disease, smoking habit, number of intensive care units (icus) beds and sub intensive care beds along with the quality of the health service. in addition, characteristics of covid-population, to encourage more healthy life styles of individuals who are subject to quarantine measures and icu admittance, raising awareness about the seasonal flu that can maximize the number of patients visiting hospital and reaching the sars-cov-2 colonization acting as a vector, protecting medical personnel who could contribute to dissemination of the infection and avoiding simultaneous transmission which can cause momentary health system failure 4 . the experience of dealing with covid-19 in brazil may give a new perspective since the country is dealing with many issues at the same time including social, political and genetics (admixed population with high variability at genome level) aspects, as follow: (i) brazil has many risk groups as described by world health organization (who) like those older than 60 years and with prognostic comorbidity, which may occur when diseases predispose the patient to (ii) brazil is a continental country with a population that is different in each region based on social behavior, genetics (each region has a different level of ancestral contribution of african, caucasians and indigenous genomes) and economic backgrounds raising the need for different medical and social managements in each area. all regions in brazil have already seen covid-19 cases and there is no medical support for all which takes into consideration particular state characteristics. in addition, brazil does not have formal data on icu beds and sub intensive care beds; besides that, the number of beds is distributed between private and public health systems. the number of patients needing the public health system is higher than for private health care. in the early stages of covid-19 disease, before community infection, the number of hospitalizations in the private system was higher than in public health system conforming with the disease origin and type of infection and its placement. between the influenza virus subtype (h1n1) pandemic (2009) and covid-19, brazil lost ~34,500 hospital beds. in approximate the number of hospital beds in the country fell approximately from 460,920 to 426,380 in the interval between the two pandemics. the fall occurred in the unified health system (sus), which lost 48,530 service spaces. in the same period, tropical countries, brazil may have a different severity and/or disease progression considering the climate markers as discussed before. in addition, in our country, there is high amplitude of lethality among states varying from zero at tocantins to 16% at piauí. also, são paulo state represents the state with highest number of cases and a lethality of 6.8%. the lethality index will change after concluding the diagnosis by real-time pcr in mild, severe cases and deaths related with respiratory symptoms close to covid-19. however, brazil is testing only severe cases and the total number of patients is underestimated; (iv) brazil is formally an admixed population including african, caucasians and indigenous features. there is also a variability in the contribution of each offspring by region from the brazil collaborating with genetic diversity that leads to a wide phenotypic expression. in those cases, the phenotype response to covid-19 can diverge among regions and, concomitantly, genetics features behind each subpopulation from brazil; (v) there is a social and economic disparity among regions corroborating several issues related with covid-19 pandemic such as availability of diagnostic tests, number of icus, access and understanding of information about the disease, and the decisions to control the pandemic; (vi) brazil presents great urban low-income conglomerates known as "favelas" where many people live in precarious condition with no access to health, social and financial support. favelas comprise ~3.7% (vii) in brazil, scientific research has been suffering from reduction in the financial support to research and scholarships. in addition, the universities, mainly federal and public, experienced a setback in recent years. this whole process confounds the difficulties of dealing with the covid-19 pandemic because brazil has many university hospitals which have financial limitations in terms of performing covid-19 diagnosis and resources to deal with the disease. some agencies are now making an effort to investigate covid-19, but we will have a limited amount of funding for studies in other areas; (viii) during recent years, the level of education of the brazilian population has hugely improved; however, the quality is not totally proven. the academic levels corroborate the low understanding about the covid-19 pandemic and the importance of social changes such as self-isolation at home; (ix) throughout the whole country there has only been genetic diagnosis in cases of severe covid-19 , leading therefore, to a very high number of undiagnosed patients. the undiagnosed patients relate to a higher index of infection and dissemination within the population which negatively affects disease control, postpones quarantine, and has further negative effects on the economy. the use of realtime pcr to confirm the disease may be the best choice for isolating confirmed patients and giving time to treat severe patients at utis. in this context, the main issue in treating covid-19 is when to start the treatment and to isolate the patients with positive real-time pcr even in the absence of clinical symptoms such as fever and cough. the country is not able to treat all patients correctly at the same time and due to that, brazil is going through the first stages of the infection. health professionals are worried about the next steps since the country is recording higher numbers of cases every day. also, during the month of march and april, emerging new cases of bronchiolitis at pediatric age which need treatment, interventions and hospitalizations; in addition, the h1n1 and dengue, both are a continuous health problem; for the public about the pandemic. moreover, the population has a low adhesion to quarantine and ministry health recommendations. this may contribute to higher infection rates, high demand for itus and general collapse in health with many deaths that could be avoided. brazilian population should have learned from italy and other countries with high number of cases and lethality 5 ; however, brazil is heading towards an uncertain future. as described by boccia et al. (2020) , brazil should at least follow the lessons from italy: " (1) avoid admitting patients with suspected sars-cov-2 infection to the hospital, except when they clearly require hospital care; (2) maintain strict hygienic procedures in the hospital environment; and (3) act swiftly in case of exposure of medical personnel to avoid the loss of personnel capacity." until now, brazil is learning to follow the lessons. in addition, as discussed by froes (2020), we need to update our action plans and to learn from our mistakes during the pandemic 6 . now, we are suffering the effects of the covid-19 diseasethe third global outbreak of coronavirus disease in the 21 st centuryand we cannot overestimate the potential of infectious diseases to change our habits as human living as civilization, but we can optimize the diagnosis time and efficacy, to achieve better adherence to infection control measures, to improve therapeutic and preventive options and to reduce the exposure to infectious agents such as sars-cov-2 6 . in conclusion, the virus cannot be allowed to insert itself among us and be just another agent responsible for the flu, because it has very high rates of transmission and its case-fatality is not low 7 . further studies and continued monitoring are needed to better understand the underlying mechanism of covid-19. in part, the brazilian society is going along with the quarantine, but there is pressure from the federal government to return everyone who has been in vertical isolation. in addition, covid-19 pandemic highlights the importance of science, education and support for scientific advance. science is the key to solving many problems; however, that key should be professionally used by society and government in order to resolve difficult and challenging situations. at 13 p.m global epidemiology of coronavirus disease 2019: disease incidence, daily cumulative index, mortality, and their association with country healthcare resources and economic status report of the who-china joint mission on coronavirus disease world health organization what other countries can learn from italy during the covid-19 pandemic facing covid-19 in italy -ethics, logistics, and therapeutics on the epidemic's front line and now for something completely different: from 2019-ncov and covid-19 to 2020-nman on the possibility of interrupting the coronavirus (covid-19) epidemic based on the best available scientific evidence key: cord-199107-01w8fk5f authors: savi, pedro v.; savi, marcelo a.; borges, beatriz title: a mathematical description of the dynamics of coronavirus disease (covid-19): a case study of brazil date: 2020-04-07 journal: nan doi: nan sha: doc_id: 199107 cord_uid: 01w8fk5f this paper deals with the mathematical modeling and numerical simulations related to the coronavirus dynamics. a description is developed based on the framework of susceptible-exposed-infectious-recovered model. initially, a model verification is carried out calibrating system parameters with data from china, italy, iran and brazil. afterward, numerical simulations are performed to analyzed different scenarios of covid-19 in brazil. results show the importance of governmental and individual actions to control the number and the period of the critical situations related to the pandemic. coronaviruses is related to illness that vary from a common cold to more severe diseases related to respiratory syndromes. coronavirus disease 2019 (covid-19) was discovered in a frame-by-frame description of the reality can be represented by a set of differential equations. by assuming only time evolution of state variables, ∈ ℜ , spatial aspects are not of concern, allowing to establish a governing equation of the form: ̇= ( ), ∈ ℜ . the description of coronavirus disease 2019 dynamics defines its propagation considering animals and humans transmission. different kinds of populations need to be defined in order to have a proper scenario of the disease propagation. lin et al. (2020) proposes a susceptible-exposed-infectious-removed (seir) framework model to describe the coronavirus disease 2019 . this model was inspired on the original model of he et al. (2013) for influenza. essentially, the description considers a total population of size n that contains two classes: d is a public perception of risk regarding severe cases and deaths; and c represents the cumulative infected cases. in addition, s is the susceptible population, e is the exposed population, i is the infectious population and r is the removed population that includes both recovered and deaths. a simplified version of the model considers only person-to-person transmission, and therefore, zoonotic effect is neglected. this scenario assumes the second stage of the wuhan -china case, after the close of the huanan seafood wholesale market. emigration effect is also neglected in order to simplify the original model. therefore, the simplified version of the governing equations considers the interaction among all these populations, being expressed by the following set of differential equations where the following parameters are defined: is the mean infectious period; is the adjusted removed period, defining the relation between removed population and the infected one; is the mean latent period; is the proportion of severe cases; is the mean duration of public reaction. it should be pointed out that the parameter − defines the evolution of the nonreported removed population, which means that, if = , populations are restricted to the classical seir case. the function = ( ) represents the transmission rate that considers governmental action, represented by (1 − ); and the individual action, represented by the function (1 − ) . therefore, the transmission rate is modeled as follows, where ̂0 = 0 ( ) ( − step function employed to consider parameter variations through time. note that, it is assumed that if 0 ( ) does not exist, the term 0 ( +1) does not exist as well, considering that index m is bigger than 1. based on that, this general function can represent constant values, or different step functions. using the same strategy, it is defined the governmental action as follows: where different steps are considered defined by time instants ( ) . in addition, individual action is represented by which the intensity of responses is defined by parameter . these parameters need to be adjusted for each place, being essential for the covid-19 description. in general, the parameter definitions depend on several issues, being a difficult task. in this regard, it should be pointed out that real data has spatial aspects that are not treated by this set of governing equations. hence, this analysis is a kind of average behavior that needs a proper adjustment to match real data. besides, r li et al. (2020) evaluated wuhan situation concluding that undocumented novel coronavirus infections are critical for understanding the overall prevalence and pandemic potential of this disease. the authors estimated that 86% of all infections were undocumented and that the transmission rate per person of undocumented infections was 55% of documented infections. this aspect makes the description even more complex. the use of step functions to define some parameters allows a proper representation of different scenarios, especially the transmission rate. it is also important to observe that either governmental or individual actions have a delayed effect on system dynamics. virus mutations are another relevant aspect related to the description of coronavirus dynamics that can dramatically alter the system response, but are not treated here. numerical simulations are performed considering the fourth-order runge-kutta method. the next sections treat the covid-19 dynamics considering two different objectives. initially, the next section performed a model verification using information from china, italy, iran and brazil. afterward, the subsequent section evaluates different scenarios for the brazilian case, using the parameters adjusted for the verification cases. as an initial step of the developed analysis, a model verification is carried out using information available on worldometer (https://www.worldometers.info/coronavirus/), considering different countries (last updates: china -march 26, italy -mar 21; iran -mar 26; brazil -mar 24). the fundamental hypothesis of the analysis is that average populations of the country is of concern. therefore, it is assumed that each country has a homogeneous distribution, without spatial patterns. basically, information from china, italy, iran and brazil are employed. this information is useful to calibrate the model parameters, evaluating its correspondence with real data. table 1 presents parameters employed for all simulations. they are based on the information of the lin et al. (2020) that, in turn, is based on other references as he et al. (2010) and breto et al. (2009) . for more details, see other citations referenced therein. mean duration of public reaction 11.2 days in addition, susceptible population initial condition is assumed to be 0 = 0.9 − 0 − 0 − 0 . in addition, it is assumed that there is no recovered population initially, i.e., 0 = 0. another information needed for the model is the number exposed persons for each infected person. it is adopted that each infected person has the potential to expose 20 persons, 0 = 20 0 . transmission rate considers specific parameters for each case. nevertheless, the reference values are presented in table 2 . other parameters are adjusted depending on the case. in the sequence, the dynamics of four different countries is analyzed in order to promote a model verification. the first scenario for the model verification is based on china results. it should be pointed out that this analysis considers all cases in china, not restricted to wuhan. parameters presented in table 3 are employed for simulations with a population of n = 1.43109 and an initial state with 554 infected persons ( 0 = 554). it should be highlighted again that these parameters are average ones since they are valid for the whole country. of course, reaction time is different from the distinct parts of the country, which makes necessary to estimate this parameter based on the real data in an average way. figure 2 presents infected population evolution showing a good agreement between simulation and real data. due to chronological issues, chinese case is the one with a large number of real data, which makes it useful to establish a comparison of the model prediction error. figure 3 presents daily errors from china, highlighting the average and maximum errors. note that the maximum error is less than 28%, with an average error of 13.58%. for the following three cases, italy, iran and brazil, it is assumed that the second stage of governmental action has not been reached yet. therefore, it is represented by a step function = [0, 0.4239], which means that (2) is neglected and 3 does not exist. italian case is now in focus considering parameters presented in table 4 with a population of n = 60.48106 and an initial state with 20 infected persons ( 0 = 20). a step function is considered to define the nominal transmission rate, 0 , due to extreme governmental actions that have not been effective until present days. figure 4 presents the infected population simulation compared with real data, showing a good agreement. figure 5 presents daily errors from italy, highlighting the average and maximum errors. for this case, the maximum error is less than 19%, with an average error of 10.60%. (1) figure 4 : italy -infected population through time. iran case is now treated considering the parameters presented in table 5 with a population of n = 81.16106 and an initial state with 20 infected persons ( 0 = 20). results are presented in figure 6 showing a good agreement with real data. figure 7 presents daily errors, highlighting the average and maximum errors. although the average error is 15.46%, the maximum error is around 42%, which is a large value. nevertheless, it should be observed that the big values are related to the beginning of the predictions, probably due to problems with the original data. (1) 24 days figure 6 : iran -infected population through time. brazilian case is now of concern considering parameters presented in table 6 with a population of n = 209.3106 and an initial state with 10 infected person ( 0 = 10). figure 8 presents the infected population evolution showing that the same trend of the other cases is followed, being enough to have a general scenario. it should be highlighted that brazilian outbreak is in the beginning, with information that is not enough for a better calibration. (1) 17 days figure 8 : brazil -infected population through time. this section has the objective to investigate different scenarios related to covid-19 dynamics in brazil. parameters adjusted on the previous section are employed to evaluate different scenarios varying governmental and individual reactions. it should be pointed out that this adjustment does not have enough information, but it is possible to perform, at least a qualitative analysis of the covid-19 dynamics in brazil. initially, two different transmission rates are defined: naive scenario, without intervention ( = = 0); and with governmental and individual actions ( ≠ 0; ≠ 0). figure 9 presents numerical simulations together with the real data that is presented just for the first days. the same parameters presented in table 6 are employed assuming (2) = 37 days. a logarithm scale is adopted since the naive scenario has a dramatic increase of the infected cases. besides the big difference between both cases, it is clear the huge impact of variations on the transmission rate function that represents governmental and individual actions. it is noticeable that the effective actions tend to reduce the infected population, reducing the final crisis period as well. nowadays, one of the most relevant issue to be discussed in terms of propagation is the governmental and individual actions. a parametric analysis is of concern considering distinct scenarios related to intervention. scenarios defined by the variation of the intervention moments is initially treated. the moment of the governmental action start, represented by parameter (1) (day), is analyzed in figure 11 , considering the following values: 17, 22, 27 and 32 and (2) is assumed to be 20 days after (1) . note that the delay to the start of the governmental action dramatically alters the response, increasing the number infected population and its duration. the same conclusion can be established considering the second governmental action, represented by (2) (day), presented in figure 12 that shows the same trend considering a different set of start instants: 37, 42, 47 and 52. a mathematical model based on the susceptible-exposed-infectious-recovered framework is employed to describe the covid-19 evolution. a verification procedure is performed based on the available data from china, italy, iran and brazil. afterward, different scenarios from brazil is analyzed. results clearly show that governmental and individual actions are essential to reduce the infected populations and also the total period of the crisis. the mathematical model can be improved in order to include more phenomenological information that can increase its capability to describe different scenarios. nevertheless, it should be pointed out that the mathematical model and its numerical simulations are important tools that can be useful for public health planning. time series analysis via mechanistic models a mathematical model for simulating the phase-based transmissibility of a novel coronavirus inferring the causes of the three waves of the 1918 influenza pandemic in england and wales plug-and-play inference for disease dynamics: measles in large and small populations as a case study early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia china with individual reaction and governmental action substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov2) dynamics of coronavirus infection in human pattern of early human-to-human transmission of wuhan chaos and order in biomedical rhythms 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 the support of the brazilian research agencies cnpq, capes and faperj. since this work was developed during a quarantine period, the authors would like to express their gratitude to familiar support that, besides the patience, helps to collect available information. therefore, it is important to acknowledge: raquel savi, rodrigo savi, antonio savi and bianca zattar. key: cord-351885-hjw1940x authors: zhang, s. x.; wang, y.; afshar jahanshahi, a.; jia, j.; haensel schmitt, v. g. title: first study on mental distress in brazil during the covid-19 crisis date: 2020-04-23 journal: nan doi: 10.1101/2020.04.18.20070896 sha: doc_id: 351885 cord_uid: hjw1940x objective: we aim to provide the first evidence of mental distress and its associated predictors among adults in the ongoing covid-19 crisis in brazil. methods: we conducted a primary survey of 638 adults in brazil on march 25-28, 2020, about one month (32 days) after the first covid-19 case in south america was confirmed in sao paulo. results: in brazil, 52% (332) of the sampled adults experienced mild or moderate distress, and 18.8% (120) suffered severe distress. adults who were female, younger, more educated, and exercised less report-ed higher levels of distress. the distance from the brazilian epicenter of sao paulo inter-acted with age and workplace attendance to predict the level of distress. the typhoon eye effect was stronger for people who were older or attended their workplace less. the most vulnerable adults were those who were far from the epicenter and did not go to their workplace in the week before the survey. conclusion: identifying the predictors of distress enables mental health services to better target finding and helping the more mentally vulnerable adults during the ongoing covid-19 crisis. the first case of covid-19 in south america appeared in são paulo in brazil on february 26, 2020. while the initial cases were imported from italy to são paulo -the economic engine of brazil with a metropolitan population of 22 million, covid-19 quickly spread across brazil, reaching 2,433 cases in a month. as cases spread, so did the distress associated with the virus. 1, 2 research is starting to identify the potential breakout of large-scale mental health issues. [3] [4] [5] [6] early evidence from china revealed the prevalence of mental health issues among adults during the covid-19 outbreak. [7] [8] [9] despite the early evidence from china, countries vary in their medical systems and resources, cultures, the covid-19 situation, and their restrictive measures, 10 and hence research can identify the predictors of mental health in individual countries to enable effective identification of mentally vulnerable groups during the covid-19 crisis. 11 this paper aims to provide the first evidence of mental distress and its predictors among adults in brazil during the covid-19 crisis. building from early research evidence on mental health in china and iran, where the covid-19 outbreak occurred earlier, 7, 8, 11 we explore several predictors of distress during the covid-19 crisis in brazil. in particular, we examine individuals' distance from são paulo -the city most affected by covid-19 in brazil. as the covid-19 crisis continues to impact brazil, we hope this research identifies useful predictors to help mental health professionals to be more targeted in locating the more mentally vulnerable individuals in the covid-19 outbreak to provide timely assistance online or via telephone. the first confirmed case of covid-19 in south america was a brazilian who returned from italy to são paulo on february 21, 2020. 12 são paulo is the biggest city and the economic center of brazil. due to its centrality in the brazilian transportation network, são paulo also became a center for the spread of covid-19 in brazil. 13 são paulo had the highest number of confirmed cases in brazil and was the first city in brazil to implement a lockdown in an attempt to slow down the spread of the virus on march 22. about one month after the first covid-19 case in brazil, we conducted an online crosssectional survey on march 25-28, 2020. during the survey dates, the total confirmed cases in brazil increased from 2,433 to 3,904, and deaths increased from 57 to 114. on march 25, são paulo accounted for more than a quarter of the total confirmed cases in brazil, and this proportion increased to one third on march 28. the survey was approved by tongji university, and we pretested the survey with five adults from brazil (not included in the main sample). the survey was voluntary and we promised the participants confidentiality and anonymity of their responses. a total of 638 adults from various parts of brazil completed our survey. we assessed the participants' socio-demographic characteristics, including gender, age, educational level, the number of children under 18 years old, geographic location, whether they were covid-19 positive, their exercise hours per day during the past week, and their workplace attendance. using the participants' location, we calculated their individual distance from são paulo, the epicenter of covid-19 in brazil, and their distance from the epicenter ranged from 0 to 3,318 km. we assessed distress using the covid-19 peritraumatic distress index (cpdi) 14 , which was specifically designed to capture distress during the covid-19 outbreak. cpdi consists of 24 questions, with the possible score ranging from 4 to 100 (normal: 4-27, mild or moderate: 28-51, severe: 52-100). we had the survey back-translated from english to portuguese. the portuguese version of the survey can be found in the online appendix. the cpdi had a cronbach's alpha of 0.87 in the brazil sample. . 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 certified by peer review) the copyright holder for this preprint this version posted april 23, 2020. were female, 78.7% (502) reported negative for covid-19, 0.9% (6) reported positive, and 20.4% (130) were unsure whether they had covid-19. in terms of exercise during the past week, 57.7% of the participants had not exercised; 21.9%, 6.9% and 5.2% of the participants reported exercising 1, 2 and 3 hours per day during the past week respectively; and 4.1% reported exercising more than 5 hours per day. the participants reported their workplace attendance by answering the question "how many days did you actually go to work in your office in the past week?". of the sample, 60.0% (383) of participants were not in the office at all in the past week, while 28.8% (184) were in the office for fewer than five days last week, 7.9% (50) went to the office for five days, and the remaining 3.3% (21) went for six or seven days. the mean (sd) score of cpdi in the sample was 37.64 (15.22), higher than the cpdi of 23.65 (15.45) reported in china from january 31 to february 10, 2020. 14 the difference in the mean values between the samples in brazil and china is 14.33 (t=23.07; p<0.0001; 95% ci: 12.80 to 15.18). the mean cpdi of sampled adults in brazil is also significantly higher than the mean cpdi of 34.54 (14.92) of adults in iran on february 28-30, 2020 (t=4.09; p<0.0001; 95% ci: 1.61 to 4.59). 11 based on the cut-off values of distress in cpdi, 52.0% of sampled adults in brazil experienced mild or moderate distress, and 18.8% experienced severe distress, compared to 47.0% and 14.1% in iran and 29.3% and 5.1% in china respectively. females experienced more distress than males (β=-8.43, p=0.000, 95% ci: -10.73 to -6.13). even though covid-19 has a higher fatality rate in the elderly, younger people reported a higher level of distress (β=-2.79, p=0.000, 95% ci: -4.03 to -1.53). adults who were more educated (β=1.93, p=0.000, 95% ci: 1.01 to 2.86) and exercised less (β=-1.47, p=0.000, 95% ci: -2.19 to -. 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 this version posted april 23, 2020. . 0.75) reported a higher level of distress. family size (p=0.164) and workplace attendance (p=0.634) failed to predict cpdi directly. we analyzed the relationship between individuals' distance from the epicenter and cpdi, as well as how this relationship was contingent on their age and the number of days in their workplace during the past week. the relationship between individuals' distance from the epicenter and their distress depended on individuals' age (model 1 of table 1 ). first, in brazil we do observe a "typhoon eye effect" -mental health issues increase with distance from the epicenter, akin to a typhoon, where the effect is stronger in the periphery than in the center. this typhoon eye effect was stronger for older adults (β=1.16, p=0.049, 95% ci: 0.00 to 2.31). we further broke down the typhoon eye effect by adults' age brackets. the relationship between the distance from the epicenter and distress was significantly positive among older adults (e. figure 1(a) shows the predicted scores of cpdi by gender, age, education, family size, workplace attendance, and distance from the epicenter. the 95% confidence intervals of cpdi in many groups based on these predictors were higher than the cutoff value of moderate distress at 28. for . 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 this version posted april 23, 2020. since individuals' distance from the epicenter interacted with their age to predict cpdi level, we plotted the cpdi level based on the interaction of these two factors in figure 1 similarly, figure 1 (c) shows the cpdi level based on the interaction between individuals' distance from the epicenter and their workplace attendance. the most vulnerable groups during the covid-19 outbreak were those who were far from the epicenter and did not go to their workplace during the past week (e.g. at 3,300 km from the epicenter: mean=43.06, 95% ci: 38.16 to 47.95; at 2,200 km from the epicenter: mean=40.96, 95% ci: 37.98 to 43.95). the distress level was the lowest among people who lived 3,300 km from the epicenter and attended their workplace every day during the past week (mean=24.68, 95% ci: 11.55 to 37.81). our findings reveal a high prevalence of distress among adults during the early stage of the covid-19 crisis in brazil. over half (52.0%) of the adults experienced moderate psychological distress and 18% experienced severe distress. the mean of cpdi of adults in brazil was also worse than the means in china and iran. individuals who were female, younger, more educated, or exercised less had more distress. it is worth noting that two predictors of distress in brazil, age and education, did not predict distress in the samples in iran. . 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 this version posted april 23, 2020. the distance from the epicenter is emerging as an interesting predictor of mental health in the crisis literature, and this study found the distance effect depended on individuals' age and workplace attendance. the positive association between the distance from the epicenter and distress, i.e. the "typhoon eye effect", was significant only in age groups of 46 years and above. this result might be because the mortality of covid-19 varies by age group. the typhoon eye effect was significant only among participants who did not attend their workplace. surprisingly, the effect reversed to become a ripple effect for those who attended their workplace every single day in the last week. there are possible explanations from many perspectives, including the meaning and fulfillment associated with work, more potential social interactions from going out to work, and less time and dependence on information from online and social media. the key contributions of this research are to help identify the predictors of those who are more vulnerable mentally during the covid-19 crisis to enable more targeted mental health services. we found gender, age, education, exercise, and distance from the epicenter all predicted distress in adults in brazil during the covid-19 crisis. in particular, this study shows the predictive effect of the distance from the epicenter varied depending on the age and workplace attendance of each individual. the findings that age and workplace attendance attenuated, and even reversed, the typhoon eye effect is particularly noteworthy to the literature and mental health service providers. there are several limitations of this study. first, our sampling is not nationally representative, because our aim was to provide rapid evidence on mental health and its predictors to enable rapid screening of the mentally vulnerable in the ongoing covid-19 outbreak in brazil. it is worth investigating if the level and the predictors of mental health change as the outbreak continues. second, brazil is a large country, and we sampled individuals from 0 to over 3,000 km from são paulo to cover various regions in brazil. it remains to be seen to what extent distance from the epicenter is a factor in other countries, most of which are smaller and have their own distinct geographical features. 8 . 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 this version posted april 23, 2020. . https://doi.org/10.1101/2020.04.18.20070896 doi: medrxiv preprint in conclusion, this study provides the first empirical evidence of mental distress and its predictors in adults in brazil during the covid-19 crisis. we hope this research not only helps mental health professionals but also encourages more research on mental health conditions and predictors during the covid-19 crisis in brazil, latin america, and beyond. 15 . 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 this version posted april 23, 2020. . 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 this version posted april 23, 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 april 23, 2020. . note: n=638. *p < 0.05; **p < 0.01; ***p<0.001. the scores of cpdi in this sample range from 6 to 80. . 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 certified by peer review) the copyright holder for this preprint this version posted april 23, 2020. . https://doi.org/10.1101/2020.04.18.20070896 doi: medrxiv preprint . 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 certified by peer review) the copyright holder for this preprint this version posted april 23, 2020. . https://doi.org/10.1101/2020.04.18.20070896 doi: medrxiv preprint . 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 certified by peer review) the copyright holder for this preprint this version posted april 23, 2020. . https://doi.org/10.1101/2020.04.18.20070896 doi: medrxiv preprint . 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 certified by peer review) the copyright holder for this preprint this version posted april 23, 2020. . psychological interventions for people affected by the covid-19 epidemic the global community needs to swiftly ramp up the response to contain covid-19. the lancet reflections about the impact of the sars-cov-2/covid-19 pandemic on mental health mental health: why it still matters in the midst of a pandemic pandemic fear'' and covid-19: mental health burden and strategies why psychiatric treatment must not be neglected during the covid-19 pandemic unprecedented disruption of lives and work: health, distress and life satisfaction of working adults in china one month into the covid-19 outbreak geographical distance to the epicenter of covid-19 predicts the burnout of the working population: ripple effect or typhoon eye effect? immediate psychological responses and associated factors during the initial stage of the 2019 coronavirus disease (covid-19) epidemic among the general population in china the global community needs to swiftly ramp up the response to key: cord-339616-4ctpq5v3 authors: de carvalho, carolina abreu; viola, poliana cristina de almeida fonseca; sperandio, naiara title: how is brazil facing the crisis of food and nutrition security during the covid-19 pandemic? date: 2020-10-12 journal: public health nutrition doi: 10.1017/s1368980020003973 sha: doc_id: 339616 cord_uid: 4ctpq5v3 the goal of this commentary is to expose the situation of food and nutrition security (fns) in brazil in the context of the covid-19 pandemic by providing a critical analysis of this scenario and suggesting ways to move forward. when covid-19 arrived in brazil, a crisis scenario that incorporated economic, social and political aspects became highly visible. this scenario fostered unemployment, poverty and hunger. besides that, it exposed multiple vulnerabilities that were getting worse over the past few years prior to the pandemic. in this context, covid-19 found in brazil a fertile ground for its dissemination and community transmission. the impacts of the suspension of many commercial activities and other economic sectors due to the pandemic were quickly felt socially and economically in brazil. some of the actions carried out by the brazilian government included the emergency aid payment and exemption from payment of energy bills for vulnerable individuals, release of funds for programmes for the direct purchase of food from family farmers, delivery of school food kits directly to students despite the closure of schools and publication of sanitary rules for the operation of restaurants. however, these actions are still insufficient, slow and not sufficiently coordinated to contain the progress of the food and nutritional insecurity crisis in brazil. the covid-19 pandemic highlights the urgency for the brazilian government to again prioritise the fns agenda. this includes implementing mechanisms to ensure the human right to adequate food and expanding existing fns programmes. the concept of food and nutrition security (fns), as adopted in brazil, was created democratically and with express participation of civil society. it is considered complex, comprehensive and innovative as the dimensions 'food' and 'nutrition' are combined into a single concept (1) . a human rights approach to fns, as committed to by brazil, establishes the responsibility of the country to promote, provide, respect and protect this right. however, by analysing the history of the political agenda of fns, it is possible to observe a dismantling of the intersectoral policies that were created in order to ensure this right. an expression of this dismantling was the termination of the national council for food and nutrition security (consea) in january 2019, an important venue for dialogue and articulation between civil societal needs and the governmental priorities (2) . when consea was a section of the national system for food and nutrition security (sisan), it operated on an agenda that was considered strategic in guaranteeing the fns led brazil to be left off of the hunger map in 2014 (3) . the termination of consea jeopardised the decisive agenda that was being consolidated throughout the country and created the possibility of brazil returning its place on to the hunger map (2) . when covid-19 arrived in brazil, a crisis scenario that incorporated economic, social and political aspects became highly visible. this scenario fostered unemployment, poverty and hunger. the fight against food insecurity in brazil was interrupted with the adoption of austerity measures, such as the national amendment 95/2016 (4) , which reduced public expenditure on social policies, in addition to labour and social security reforms, which represents a scenario of violation of human rights that are being aggravated by the current pandemic. in this context, the goal of this commentary is to expose the situation of fns in brazil in the context of the covid-19 pandemic by providing a critical analysis of this scenario and suggesting ways to move forward. fao estimates that the expected number of people in food insecurity by 2020 will increase from 135 million to 265 million due to the covid-19 pandemic (5) . according to the fao report, the countries most affected by the pandemic are those that have already faced serious food insecurity problems due to conflicts and wars, climate change, and economic crises. in these countries, the risk of food supply chain interruption is imminent, thus damaging farmers' incomes and the food supply of cities (5) . in mexico, the country with the third largest number of deaths caused by covid-19, behind only the united states and brazil (until august 2020), vilar-compte et al. (6) pointed to the absence of interventions and social protective actions by the federal government, especially of those aimed at children. in the united states, the country with the highest number of covid-19 cases and deaths in the world, trillion-dollar packages have been released to support the country's economy companies and maintain jobs. direct income support, increased unemployment benefits and additional support for federal food assistance programmes in the united states have also been implemented (7) . in brazil, the covid-19 pandemic exposed multiple vulnerabilities that have been festering over the past few years prior to the pandemic. the latest population surveys carried out in brazil in the years 2004, 2009 and 2013 indicate that there is regional inequality in the distribution of food insecurity with the north and northeast regions being the most affected (8) . these regions are characterised by a scenario of inadequate access to essential and basic services, which exposes them both to food and nutritional insecurity and to the spread of covid-19. this inadequacy is demonstrated by the fact that these were also the regions most affected at the beginning of the pandemic. this finding shows that the social determination of food insecurity in brazil is similar to that of the covid-19 pandemic, affecting mainly people in racial, social, economic and sanitary vulnerability (9) . in this context, covid-19 found fertile ground in brazil for its dissemination and community transmission. the impact of the suspension of many commercial activities and other economic sectors due to the pandemic was quickly felt socially and economically in brazil. the comparison of the final quarter of 2019 and first quarter of 2020 revealed an increase in the unemployment rate, which was the highest in the northeastern region and caused a higher number of poor and extremely poor people in brazil than was already there (10) . by june 2020, more than 10 million workers had already had their job contracts suspended or had their working hours and salaries reduced, and the country had more than 1·2 million people unemployed. the increase in unemployment rates and poverty in the country in addition to the increase in prices of natural or minimally processed food during the pandemic (11) indicate the addition of millions of brazilians to the group of people who are vulnerable to food and nutrition insecurity. it is important to highlight that at the beginning of the pandemic, the population was concerned with the lack of food, but currently, no signs of food shortage in brazil are visible. therefore, although no interruption in food supply occurred, brazilians with compromised incomes during the pandemic may have problems accessing food as they are unable to afford it. a study conducted in brazil by the unicef and the brazilian institute of public opinion and statistics (ibope) from 3 july 2020 to 18 july 2020, showed that during the pandemic, one in five brazilians aged 18 years or older (33 million) experienced an episode of having no money to buy food when their income ran out. this study also reports that about nine million brazilians were unable to have a meal because there was no food or money to buy one (12) . given the evident and expected impacts caused by the covid-19 pandemic in relation to the population's fns, the brazilian government responded with a few actions although they were slow and uncoordinated. furthermore, it is important to stress that the majority of these actions were pressured and amplified by the national congress. the main governmental action to minimise the impacts of the pandemic over the income of the most vulnerable families was the introduction of an emergency aid payment in the amount of us$120 over a 5-month period for informal workers, individual entrepreneurs, independent workers and the unemployed. the initial proposal of the federal government was only us$40, but the amount was increased after congressional intervention. up to 3 august 2020, 66·2 million brazilians had already received this payment. however, the way this aid has been operationalised has been heavily criticised due to the difficulties in access to registration for some population groups and delays in processing registrations (11) . moreover, an announcement about the expansion of the income transfer programme bolsa família, aiming to release more than us$680·000·000 has been made. however, until 18 august 2020, only 12·2 % of the amount allocated to the expansion had been used (13) . another measure implemented to preserve family incomes was payment exemption of up to 220 kwh/month towards the electricity bill of low-income families from 1 april to 30 august. the program for food acquisition (paa) is one of the main fns programmes in brazil. this programme's main goal is to promote access to food and encourage family agriculture. due to covid-19, this programme received a budget supplementation of 500 million reais, which is considered insufficient (14) , especially considering the scenario caused by the pandemic, and delayed since the publication of the provisional measures only happened almost 2 months after covid-19 hit brazil (11) . this emergency act took place after recent stripping of resources allocated to paa, which were reduced from us$117·200·000 in 2012 to us$12·600·000 in 2019 (14) . the national school nutrition program (pnae) (3) is the oldest public policy for fns in brazil. with schools closing as a strategy to reduce the spread of the virus, millions of students have become vulnerable to food and nutrition insecurity. as a way to mitigate the effects of the pandemic on the fns of this part of the population, the federal government authorised the use of school nutrition resources for the distribution of food to students. in this programme, 30 % of the purchased food should come from family agriculture. therefore, purchasing of this food even during the pandemic allows the continuity of the outflow of production and farmers' income. with respect to the sanitary and hygienic aspects of fns, the food supply chain and the food industry also needed to adapt to changes in food safety protocols imposed by the pandemic. although there is little evidence of transmission of covid-19 through food, it is important to highlight that there are potential sources of risk of contamination along the food supply chain that involve many people, surfaces and environments. in this sense, to ensure food and environmental safety, strict safety protocols are necessary (15) . the national health surveillance agency (anvisa) has published sanitary guidelines in relation to covid-19 and the good practices for manufacturing and manipulation of food (16) . however, we believe that the capacity of food safety inspectors is limited when it comes to implementing the recommendations in this publication after considering that before the pandemic anvisa already had difficulties in satisfying all of its inspection demands. the impact of the pandemic on the fns of the brazilian population was strengthened as the country faced a previous scenario of progressive weakening of fns policies marked by the termination of consea, budget cuts for programmes for promotion and support of family agriculture, and the disbanding of these programmes. these policy and institutional changes undermine the capability of the state to satisfy the demands that the covid-19 pandemic has imposed on the fns of the population. however, in the current scenario, we believe that a few actions would result in better responses to fns protection. among those, we highlight the urgent need for actions imposed by the state and then coordinated among the three levels of the government. the need for coordinated and intersectoral actions to address fns is even more important during a pandemic. another recommendation is to harness the great potential of primary healthcare to implement fns programmes in territories. primary health care has been underused when it comes to identification and attention to the needs of families regarding fns. mobility restrictions recommended as a way to prevent the dissemination of covid-19 and the work-from-home conditions imposed on thousands of brazilians in addition to full-time childcare could make families seek more practical and quicker foods, such as ultra-processed and fast food items. in the context of the covid-19 pandemic, it is possible that the population will further increase the intake of ultra-processed foods and aggravate the situation of food insecurity thus leading to worsening of the dietary quality (12) . evidence that the diet has worsened during the pandemic in brazil can be found as there was a decrease in the consumption of fruits and vegetables and an increase in the consumption of several types of ultra-processed foods. together with the deterioration of dietary quality, increased sedentary behaviour demonstrated by longer screen time and a drastic decrease in physical activity practice has been reported in brazil during the pandemic (12, 17) . the perpetuation of these inadequate food and lifestyle habits during the months of quarantine has resulted in an increase in the prevalence of overweight and other chronic noncommunicable diseases, such as hypertension, cardiovascular diseases and diabetes. therefore, actions to promote healthy eating and physical activity in the context of social isolation must be implemented. the weakening and the attempt to disarticulate social control, especially represented by the termination of consea, is also an aspect that limits and hinders the capability to respond to actions for improving fns during the pandemic. nevertheless, some of the actions that have food and nutrition security and covid-19 taken place to date happened under great pressure from civil society since a remnant of organised structure of social control still exists. finally, with the impacts of the covid-19 pandemic, another action which has become even more urgent is that the government again should prioritise the fns agenda and update the national plan for food and nutrition security (pnsan). the last one ended in 2019, and the replacement that was supposed to be implemented from 2020 to 2023 has not been created. updating the pnsan would allow for the creation of coordinated actions with cities and municipalities and budget transfers that are aligned with the needs of the programmes and public policies. this would ensure again the realisation of the human right to adequate food and expand fns programmes. strengthening human rights, including fns, is essential for the structuring of a more equitable society, and it has a legal basis through the constitution. however, it is a historical challenge that will become even more complex in the context of a pandemic and runs counter to political will and commitment of leaders and nations. history and challenges of brazilian social movements for the achievement of the right to adequate food the dissolution of the brazilian national food and nutritional security council and the food and nutrition agenda strengthening the enabling environment for food security and nutrition conventionality control and amendment 95/2016: a brazilian case of unconstitutional constitutional amendment fao (2020) policy brief: the impact of covid-19 on food security and nutrition costing of actions to safeguard vulnerable mexican households with young children from the consequences of covid-19 social distancing measures food insecurity and covid-19: disparities in early effects for us adults trends and factors associated with food insecurity in brazil: the national household sample survey black population and covid-19: reflections on racism and health continuous national household sample survey-continuous pnad the future at the kitchen table: covid-19 and the food supply united nations children's fund (2020) primary and secondary impacts of covid-19 on children and adolescents brazilian federal government (2020) monitoring federal spending on combating covid-19 the food acquisition program (paa) as a strategy to face the challenges of covid-19 safety of foods, food supply chain and environment within the covid-19 pandemic anvisa (2020) national health surveillance agency. technical note n o 18/2020/sei/giali/ggfis/dire4/ anvisa [covid-19 and good manufacturing practices in food handling /78300ec1-ab80-47fc-ae0a-4d929306e38b the covid-19 pandemic and changes in adult brazilian lifestyles: a cross-sectional study acknowledgements: not applicable. financial support: this study was financed in part by the coordenação de aperfeiçoamento de pessoal de nível superior -brasil (capes) -finance code 001. conflict of interest: none. authorship: all authors contributed equally to the formulation, production and writing of this manuscript and are fully responsible for the information contained in it. ethics of human subject participation: this commentary do not involve research with human participants key: cord-343183-5jlnw6e0 authors: sato, ana paula sayuri title: pandemic and vaccine coverage: challenges of returning to schools date: 2020-11-05 journal: revista de saude publica doi: 10.11606/s1518-8787.2020054003142 sha: doc_id: 343183 cord_uid: 5jlnw6e0 since march 2020, brazil has faced the pandemic of the coronavirus disease 2019 (covid-19), which has severely modified the way in which the population lives and uses health services. as such, face-to-face attendance has dropped dramatically, even for child vaccination, due to measures of social distancing to mitigate the transmission of the virus. several countries have recorded a substantial drop in vaccination coverage in children, especially of those under two years of age. in brazil, administrative data indicate the impact of the covid-19 pandemic on this downward trend, which was already an important challenge of the national immunization program in recent years. many children will be susceptible to immunopreventable diseases, which reinforces the need to assess the vaccine status of schoolchildren before returning to face-to-face classes. vaccination (along with other public policies, especially those aimed at expanding sanitation) has made possible to substantially decrease the number of deaths of children under five years of age worldwide 1 . widespread vaccination allowed the eradication or control of immunopreventable diseases in several regions of the world, including brazil, due to successful immunization programs [1] [2] [3] . in brazil, since the 1990s, vaccine coverage in children under one year of age had rates above 95%, which indicated the high participation of the population in vaccination and the good performance of the national immunization program (nip) 4 . the gradual implementation of the brazilian unified health system (sus) in the late 1980s allowed for a high rate of vaccine coverage through the expansion and decentralization of health services, mainly due to its principle of universal and free access to vaccination [5] [6] . throughout its history, the nip faced several challenges. in the 1980s, the first national surveys of vaccination coverage showed worse coverage in poorer segments of the population; this difference disappeared in the late 1990s, indicating that equity of access to vaccination had been reached in different socioeconomic strata of brazil 2,7,8 . however, according to the 2007 national survey, the country now has a lower coverage on both the richer and the extremely poor demographics 9 . moreover, from 2016 onwards vaccine coverage rates have declined about 10% to 20% 10,11 , due to factors not yet understood. the measles epidemic that hit several states in 2018 and 2019 is an immediate consequence of the decrease in vaccine coverage 12 . among the possible explanations for this, we have the decrease in the perception of risk of these diseases and the increased perception of risk of adverse events following immunization (aefi). this phenomenon was also recorded in other countries, due to the success of immunization programs when disease control or elimination is reached, a result of the prolonged maintenance of high vaccination coverage. thus, success itself has become a great challenge 13 . however, it is accepted that this is not the sole reason: among other factors that influenced the drop in vaccination coverage since 2016, the emergence of vaccine hesitancy is highlighted. this a phenomenon that has gained importance in various parts of the world and is characterized by the delay in accepting or refusal of the vaccine, regardless of its availability and access to health services 10,14-16 . the political and economic crisis, the decrease in government support for the sus 17 and the dissemination by social networks of distorted information about vaccines are also worthy of mention, all of which possibly contributed to the sharp drop in vaccine coverage in recent years [18] [19] [20] . in 2020, due to the pandemic of coronavirus disease 2019 (covid-19), face-to-face attendance in health services dropped dramatically in many countries; this included child vaccination, given the measures of social distancing to mitigate viral transmission [21] [22] [23] [24] [25] [26] [27] . efforts to contain the pandemic, which involve distant medicine practices and the use of other technologies in order to continue health care at home, have affected vaccination actions, which require travels to the healthcare unit 22 . parental concern in exposing children to sars-cov-2 when taking them to health services for vaccination also contributed to the decline in vaccination coverage 22, [24] [25] [26] 28 . a risk-benefit study in african countries showed that avoidable deaths from routine vaccination outweigh the excess risk of death from covid-19 associated with attendance at the healthcare unit, evidencing the need for increasing vaccination coverage at this time 21 . child vaccination coverage has declined sharply during the pandemic in several regions of the world 26, 28 . in the usa, a considerable decline in the vaccine coverage of children was found, starting in the week after the national emergency scenario was declared (march 13, 2020). higher rates were found among children under two years of age 25 . in england, three weeks after the introduction of social distancing (march 20, 2020), there was a 19.8% drop in doses of the measles-mumps-rubella vaccine, compared to the same period in 2019 24 . in michigan (usa), completeness of the vaccination schedule for five-year olds dropped from 67.0% to 49.7% in may 2020. at 16 months, it was found that measles vaccine coverage decreased from 76.1% to 70.9% 22 . in indonesia, where immunization occurs in schools, a significant drop in coverage of the basic vaccination schedule was predicted after the closure of schools in march 2020 27 . moreover, it is known that this impact will be even more important in families with unfavorable socioeconomic conditions 26 . the world health organization (who) estimates that at least 80 million children will be susceptible to immunopreventable diseases such as measles, diphtheria and polio because of the decrease in vaccination coverage during the covid-19 pandemic 29 . it is worth remembering that outbreaks of measles were attributed to the interruption of vaccination services during the 2013-2016 ebola epidemic in west africa, causing a second public health crisis [30] [31] . the pandemic of the new coronavirus has challenged health systems around the world in providing essential services, including immunization programs, as routine vaccination and mass vaccination campaigns could contribute to the spread of covid-19 32 . on march 26, 2020, who and the pan american health organization published recommendations on vaccination during the covid-19 pandemic. the measures considered three scenarios of availability of health services and included the temporary suspension of mass vaccination campaigns during this period. it was recommended that routine vaccination be maintained in places where essential health services had operational capacity of human resources and supply of preserved vaccines, respecting social distancing and other measures to control transmission of sars-cov-2 33,34 . in brazil there was the recommendation of suspending routine immunization during the first 15 days of the influenza vaccination campaign, as this was a period in which older adults and health professionals were supposed to be vaccinated; although this was valid as a safety measure for the older population, it has generated concern among brazilian medical societies 35 . the who recognizes this fragility and recommends efforts to ensure high vaccination coverage, seeking herd immunization for preventable diseases, in such way that vaccination programs should adopt innovative measures 36, 37 . vaccination strategies in vehicles, at home or in specific rooms and well-separated from the locations of other clinical visits could be used, as well as the identification of absentees and recruitment for vaccination with the aid of electronic immunization registries (eir) 22, [24] [25] [26] 28 . eir allow greater efficiency of health services, because, in addition to providing the evaluation of vaccination coverage, they also help in routine practice and enable the convocation of absentees, thus increasing the scope of immunization 38, 39 . in addition, they are important sources of information, which can be applied in the evaluation of performance indicators and in the development of epidemiological research 38, 40 . in 2020, researchers from countries such as the usa and the united kingdom evaluated in real time the decline in vaccination coverage and the number of doses applied during the covid-19 pandemic through eir. with this quick identification, it is possible to quickly adopt strategies in the face of this challenge 22, 24, 25 . with the emergence of many radical groups worldwide that deny the importance of the pandemic and its associated mitigation measures, vaccine hesitancy might acquire more strength, especially considering the availability of vaccines for covid-19 in the near future that will have an important role in dealing with this disease 41 . the safe resumption of day care centers and schools should be a national priority. children have lost fundamental benefits of social, educational and developmental nature. for many parents, it will not be possible to return to work if these institutions remain closed, thus exacerbating social inequities. several individual practices (use of masks, hygiene, social distancing, temperature measurement etc) as well as environmental ones (maximum capacity and layout of classrooms, cleaning etc) will be necessary to prevent the transmission of sars-cov-2 between schoolchildren and staff, including in transportation to schools 42, 43 . however, in addition to care for covid-19 44 , the american academy of pediatrics recommended that schools, health services, and local health authorities promote child vaccination well before the beginning of the school year. it is important that children receive vaccines at the recommended age and be updated in case of vaccine delay due to the pandemic 45 . this recommendation should be considered in other countries, including brazil. in brazil, the pandemic was an additional challenge for the return to schools due to the abovementioned immunopreventable diseases, as we recently faced a consistent drop in vaccination coverage and a wide epidemic of measles that reached several states and amounted for thousands of cases. this situation has worsened in 2020, which until august had registered more than 7,000 confirmed cases of measles 46 . according to data from the nip information system (is-nip), when comparing the number of first doses of the pentavalent vaccine applied in march 2020 with march 2019, we found a decrease of 27% ( figure) [10] [11] . these data indicate that the return to classes may increase the risk not only of the expansion of measles epidemics throughout the country, but also of the reemergence of other already controlled diseases, such as diphtheria and the whooping cough. studies show that outbreaks of diphtheria occur when vaccination coverage drops due to migration and/or political instability, emphasizing that it is a disease of relevant lethality [47] [48] [49] . thus, it is evident that, before the progressive return of face-to-face school activities, intensive actions to assess the vaccine situation of this population will be necessary in order to recover sufficient vaccination coverage to prevent or reduce the spread of immunopreventable diseases 45 . innovative instruments, such as eir, can be useful for real-time assessment of vaccination coverage, as well as to warn about immunization and rescue individuals with vaccine delay 22, 24, 25, [38] [39] [40] . to date, there are no studies on the impact of covid-19 on the decline in vaccine coverage. delays in child vaccination (a demographic that should have been immunized in the most intense moment of social distancing) are also yet to be studied, even in other countries. moreover, despite the universal access to child vaccination achieved by the nip in the last decade, this impact will probably be greater in children from families with unfavorable socioeconomic conditions, due to less access to health services and information. when social distancing measures are loosened, many children will be susceptible to preventable diseases, and there will be a need to assess the vaccine situation of schoolchildren before returning to school 22, [24] [25] [26] 28, 45 . the covid-19 pandemic recalled the importance of vaccination by showing how fast a disease can spread and cause irreparable harm in societies without this defense. when a safe and effective vaccine for sars-cov-2 is available, immunization programs will have an even greater challenge of strengthening and reaching those most vulnerable 28 . world health organization. global vaccine action plan 2011-2020: review and lessons learned successes and failures in the control of infectious diseases in brazil: social and environmental context, policies, interventions, and research needs the contribution of vaccination to global health: past, present and future coberturas vacinais e doenças imunopreveníveis no brasil no período 1982-2012: avanços e desafios do programa nacional de imunizações the brazilian health system: history, advances, and challenges doenças infecciosas no brasil: das endemias rurais às modernas pandemias effectiveness of influenza vaccination and its impact on health inequalities desigualdades sociais e cobertura vacinal: uso de inquéritos domiciliares socioeconomic inequalities and vaccination coverage: results of an immunisation coverage survey in 27 brazilian capitals qual a importância da hesitação vacinal na queda das coberturas vacinais no brasil? longitudinal profiling of the vaccination coverage in brazil reveals a recent change in the patterns hallmarked by differential reduction across regions trends and spatial distribution of mmr vaccine coverage in brazil during epidemiologic methods in immunization programs vaccine hesitancy: definition, scope and determinants the emergence of vaccine hesitancy among upper-class brazilians: results from four birth cohorts vaccine confidence and hesitancy in brazil os desafios atuais da luta pelo direito universal à saúde no brasil the public health crisis of underimmunisation: a global plan of action the debate on vaccines in social networks: an exploratory analysis of links with the heaviest traffic here we go again: the reemergence of anti-vaccine activism on the internet routine childhood immunisation during the covid-19 pandemic in africa: a benefit-risk analysis of health benefits versus excess risk of sars-cov-2 infection decline in child vaccination coverage during the covid-19 pandemic -michigan care improvement registry impact of the covid-19 pandemic on emergency department visits -united states early impact of the coronavirus disease (covid-19) pandemic and physical distancing measures on routine childhood vaccinations in england effects of the covid-19 pandemic on routine eediatric vaccine ordering and administration -united states routine vaccination during covid-19 pandemic response the potential impact of covid-19 pandemic on the immunization performance in indonesia the impact of covid-19 on the routine vaccinations: refletions during world immunization week 2020 at least 80 million children under one at risk of diseases such as diphtheria, measles and polio as covid-19 disrupts routine vaccination efforts, warn gavi, who and unicef [news release reduced vaccination and the risk of measles and other childhood infections post-ebola the health impact of the 2014-15 ebola outbreak covid-19 disrupts vaccine delivery guiding principles for immunization activities during the covid-19 pandemic. geneva: who; 2020 pan american health organization. the immunization program in the context of the covid-19 pandemic sociedade brasileira de pediatria sociedade brasileira de imunizações. calendário vacinal da criança e a pandemia pelo coronavírus. rio de janeiro: sbp pan american health organization. vaccination of newborns in the context of the covid-19 pandemic world health organization regional office for europe. guidance on routine immunization services during covid-19 pandemic in the who european region national immunization program: computerized system as a tool for new challenges monitoring vaccination coverage: defining the role of surveys sistemas informatizados de registro de imunização: uma revisão com enfoque na saúde infantil the vaccines act: deciphering vaccine hesitancy in the time of covid-19 challenges of "return to work" in an ongoing pandemic reopening primary schools during the pandemic covid-19 and school return: the need and necessity covid-19 planning considerations: guidance for school re-entry. itasca, il: aap; 2020 vigilância epidemiológica do sarampo no brasil -2020 semanas epidemiológicas 1 a 32 clinical and epidemiological aspects of diphtheria: a systematic review and pooled analysis global epidemiology of diphtheria diphtheria in the former soviet union: reemergence of a pandemic disease authors' contribution: study design and planning; data collection, analysis and interpretation; preparation and review of the manuscript; approval of the final version; public responsibility for the content of the article: apss. the authors declare no conflict of interest. key: cord-256553-iw5squ6n authors: neiva, mariane barros; carvalho, isabelle; costa, etevaldo dos santos; barbosa-junior, francisco; bernardi, filipe andrade; sanches, tiago lara michelin; de oliveira, lariza laura; lima, vinicius costa; miyoshi, newton shydeo brandão; alves, domingos title: brazil: the emerging epicenter of covid-19 pandemic date: 2020-10-21 journal: revista da sociedade brasileira de medicina tropical doi: 10.1590/0037-8682-0550-2020 sha: doc_id: 256553 cord_uid: iw5squ6n introduction: five months after the first confirmed case of covid-19 in brazil, the country has the second highest number of cases in the world. without any scientifically proven drug or vaccine available combined with covid-19’s high transmissivity, slowing down the spread of the infection is a challenge. in an attempt to save the economy, the brazilian government is slowly beginning to allow non-essential services to reopen for in-person customers. methods: in this study, we analyze, based on data analysis and statistics, how other countries evolve and under which conditions they decided to resume normal activity. in addition, due to the heterogeneity of brazil, we explore brazilian data of covid-19 from the state health secretaries to evaluate the situation of the pandemic within the states. results: results show that while other countries have flattened their curves and present low numbers of active cases, brazil continues to see an increase in covid-19 patients. furthermore, a number of important states are easing restrictions despite a high percentage of confirmed cases. conclusions: all analyses show that brazil is not ready for reopening, and the premature easing of restrictions may increase the number of covid-19-related deaths and cause the collapse of the public health system. with 13 million cases and 576,000 deaths, the largest pandemic since the spanish flu in 1918 has now reached over 200 countries in the world. covid-19, a disease caused by sars-cov-2, started in wuhan but rapidly spread across asia, europe, and america 1 . brazil, which had its first confirmed case on february 25, 2020, almost two months after the announcement of the outbreak of the disease in china, is now the country with the second highest total number of confirmed cases 2,3 . by july 14, 2020, we accounted for 1,888,000 cases and 72,000 deaths 1 . as a new disease, despite all advances in technology and rapid genome analysis, there are no scientifically proven treatments, such as drugs and vaccines, to protect people or cure infected patients. thus, the main recommendations from the world health organization (who) for the general population are to maintain social distance and hygiene habits such as the use of alcohol-based hand sanitizers and face masks, measures intended to slow the spread of the virus 4 . furthermore, social inequalities in brazil highlight the importance of higher isolation rates since the public health system cannot withstand high pressure. sus, the brazilian public health system, is responsible for the support of 80% of the population and could collapse if a considerable number of people contract the disease in a short period of time 5 . moreover, people's confidence in the government is referenced as one of the critical points in handling the pandemic successfully. nevertheless, brazil is going through a hard time in the political sphere. as examples that directly impacts the covid-19 battle, the health minister was replaced twice in two months and the country's president has been frequently seen in groups not complying with the medical community's recommendations, thereby influencing the population 6, 7 . understanding data is essential for the proper care of the population. therefore, in this study, we analyze the situation of the pandemic in other countries to explore how they dealt with the disease and under which conditions they decided to resume non-essential services 8 . by understanding the evolution of each country and the statistics in brazil, the goal of this study is to evaluate whether the tropical country is gathering knowledge from other regions and easing restrictions according to certain metrics such as the decrease in daily cases and deaths. this article is a descriptive observational study using classical statistical metrics, such as frequency and percentage. the analysis is divided into two parts. first, the aim was to characterize how brazil is evolving in the covid-19 war. for this, the brazilian data at the federal level were compared with data from other countries regarding three types of information: the number of new cases, the number of new deaths, and active cases. for this analysis, we collected data from john hopkins 9 , which allowed us to obtain the daily and total cases, deaths, and recovered patients, along with the evolution of the pandemic. active cases are not directly obtainable from the hospital database; thus, we computed them using the following equation: active_cases(x) = total_cases(x) -total_deaths(x) -total_recoveries(x), where total_cases(x), total_deaths(x), and total_recoveries(x) are the total number of positive cases, deaths, and recovered patients, respectively, until day x. the measure is a good track to understand how many patients are currently transmitting the viruses or might require hospitalization, which is important for public health policies. furthermore, we also compared the total number of cases in each country according to their size. the relative comparison is essential because countries with different sizes probably have more cases compared to smaller regions. therefore, by dividing the cases by the population size, one can understand the proportion of inhabitants of each country that contracted covid-19 and the differences and similarities among couples of countries. besides brazil, seven countries are evaluated: south korea, the united states of america, spain, italy, new zealand, germany, and china. along with the comparison of countries, we also compared the first and second positions in the worldwide rank of case numbers provided by 1 . to do this, we used the epidemiological knowledge that virus propagation within the population can fit an exponential model 10 . thus, we used computational simulations in python to fit the total number of cases of brazil and the us as an exponential curve. to perform this analysis, we used the data from the previous two weeks, the approximate period of time sars-cov-2 remains in an individual organism 11 , to obtain the exponential parameters. then, we projected the data for the next 15 days. another statistic is the testing rate for each confirmed case. testing suspected cases reduces the under-detection probability and enhances the reliability of the data. data were retrieved from our world in data 12 for each country. the results are shown in section 3.1. finally, in section 3.2, we seek to understand how covid-19 performed within the brazilian territory. disaggregating geographically by state, the analyses aimed to characterize the number of cases, the number of deaths, and their influences on population rates over the time that the virus disseminated throughout the country over 5 months (from february to july). the behavior of dissemination and danger of the virus was characterized by the contamination rate, which describes the speed of spread of the virus through the number of cases normalized by the population of each place per 100 thousand inhabitants, and the lethality rate, which describes the proportion of people who die among all those infected 13 . data were obtained from the state health secretaries' databases and along with information of absolute and relative cases for each of the main states in brazil, we also evaluated the spatial evolution of the pandemic in the state of são paulo, the most populated location in brazil. finally, we discuss the evolution of reopening measures in brazil, showing a map with coping policies for each country. the coping information was retrieved from the news and collected from https://ciis.fmrp.usp.br/covid19/. as previously mentioned, it took two months for brazil to have its first confirmed case of covid-19, which gave the country a foundation of information and knowledge to better understand the evolution of the disease, as well as the opportunity to see how other countries proceeded with reopening. first, one can start by understanding the situation in wuhan, the breakpoint of the pandemic that previously suffered from sars and the avian flu 14 . despite the recent history of respiratory diseases, covid-19 is a new challenge that is not yet fully described by science, and the prognosis of patients can be unpredictable. in order to contain the spread of the disease and a high number of deaths, the chinese government ordered a lockdown in hubei, applying severe restrictions regarding social isolation which were widely obeyed 1 . furthermore, the culture of using face masks as a routine probably helped to decrease the rate of transmission 15 . by the beginning of march, china had already less than 100 new cases per day, and, by mid-june, there were under 10 new cases per day 1 . the country was one of the first to reopen and is currently tracking new cases by applying social distancing in workplaces, constant disinfection, and temperature measuring more than once a day 16, 17 . these actions appear to be effective, considering the number of new cases shown in figure 1f . new zealand is another country that has succeeded in beating covid-19. after 24 days with no detection of covid-19, a patient was diagnosed on june 16, having contracted it in the united kingdom, meaning no local transmission had occurred in three weeks 18 . the reason for such success? travel restrictions and quarantine measures with a low level of confirmed cases 19 . prime minister jacinda ardern has demonstrated strong leadership, convincing almost five million people to respect the stay-at-home guidelines 20 . furthermore, testing and tracking were applied all over the country with the support of mobile applications that use qr codes to scan buildings and alert possible infected people 21 . after one week with zero new cases, new zealand began to ease its restrictions 22 . south korea also used technology, isolation restrictions, and extensive temperature measuring 23, 24 . in europe, germany also applied consistent rules and strategies to fight the virus, such as intensive care unit (icu) monitoring, testing, and patient tracking 25, 26 . italy was one of the countries most affected by covid-19 due to a delay in establishing restrictions in many points of the country. the 'milan does not stop' campaign, for example, ignored the isolation instructions from who in an attempt to prevent the economy from collapsing 22 . after losing control of the disease spread, a lockdown began on march 9 and lasted until may 18 27, 28 . although these countries may have established different strategies, most of them relied on who instructions, scientific evidence, and strong leadership. figure 1 shows that almost all countries are on the downside of the curve of new cases. the database of the graphs was retrieved from the john hopkins hospital 9 . the number of active cases in italy, around 13,000, is still high, which requires intense observation of health services capacity since isolation restrictions are being loosened. with no drug or vaccine, all countries must keep monitoring its cases to understand whether it is time to re-apply restrictions or if one proceed to new phases of reopening. however, one can see that brazil and the united states, the second and first countries, respectively, in the number of confirmed cases, do not follow the same patterns in the new cases/deaths and active case graphs, as shown in figures 1g and 1h . furthermore, the graph of active cases shows a steep incline, while new cases and deaths are increasing. this is also evident in figure 2a , where most countries' curves are flattening and brazil and the united states curves continue to increase. as the us and brazil rank as first and second in numbers of active cases 1 , we compared both exponential projections in an attempt to predict the future. in figure 2b , it appears that brazil will overtake the us in numbers of active cases by the end of august. such analysis considers the relative number of cases in both countries to remove population size influence. this means that besides being the country in south america with the most covid-19 cases, brazil will also have the highest number of cases worldwide. the situation is even more worrying, as brazil has a low test rate and, consequently, a high likelihood of under detection (figure 3 ) compared with countries that are coming out of lockdown. furthermore, several places in brazil are easing isolation rules and opening non-essential services, such as malls, which are usually environments with low air circulation and, therefore, conducive to the spread of the virus. it should be taken into account that brazil is a very heterogeneous country with high social inequality. the pandemic is affecting the public health system and the population in a non-uniform way, as approximately 11.4 million people live in shanty houses. the following section highlights these differences and shows more in-depth features of this enormous country. brazil, with 26 states and one federal district, is the seventh most populated country, and the fifth with the greatest territorial extension worldwide 29 . therefore, the country is inconsistently dealing with the coronavirus epidemic. each brazilian state behaves like a small country, and the segregation of analysis aims to strengthen the action plans. the following analyses considered the five brazilian states with the highest numbers in each indicator. figure 4a shows the accumulated number of cases over time. in order, the five states with the highest number of cases were são paulo, ceará, rio de janeiro, pará, and bahia. at the end of may, they recorded approximately 880,000 cases, 47% of all brazilian cases. são paulo has been the leader in the number of cases since the beginning, with approximately 173% more cases than the second ranked state, ceará. this is because são paulo is the industrial center figure 3: besides the high number of cases in brazil, the country is known for its lower testing rate. this has direct consequences on the under detection covid-19, meaning that brazil possibly has more cases than those noted by health care centers. conversely, south korea and new zealand are among the countries with the highest rates of testing and are considered successful cases in the pandemic. and the most populated area of the country, with approximately 45 million people. however, the absolute number of cases alone does not provide a complete picture of the severity and speed of dissemination. thus, figure 4b shows the contamination rate. the latter four states did not have a large accumulated number of cases, but showed high daily growth in relation to the other brazilian states. a different scenario is observed when analyzing the contamination rate, as shown in figure 4b . the measure refers to the number of cases normalized by the population of each state per 100 thousand inhabitants. since the end of april, the states of amapá, roraima, amazonas, and acre have presented high community transmission of the coronavirus. this has resulted in a new focus on the north region of brazil. none of these regions were even mentioned in previous analyses. this negative impact of this statistic was clearly seen in mid-april when the state of amazonas became the first brazilian state to be on red alert, asking for international support due to the collapse of the funeral and health system 30, 31 . with the diversity and immensity of the country, brazil has several areas and different needs that require attention. thus, it is essential to explore different indicators to capture these needs as quickly as possible. figure 4c presents the death analysis. it is expected that the number of deaths will be proportional to the number of cases. four of the states with the highest absolute number of deaths have already been mentioned as critical in previous analyses; however, the state of pernambuco is unprecedented and had more than 2,500 deaths by the end of may. together, the five states with the highest number of cases have reported almost 20,000 deaths and represent 75% of total brazilian deaths. regarding daily case information, the highest number in the country occurred in são paulo on june 3 when 609 deaths due to covid-19 were recorded in 24 hours. hospital morgues located in rio de janeiro, which also has a high number of daily deaths, are dealing with overcrowding and accumulating bodies day after day 32 . the last indicator explored in this subsection is the lethality rate, as shown in figure 4d . the lethality rate is the ratio between the number of deaths and the total number of cases of a disease in a given period; it represents the risk that people with the disease have of dying from the disease 13 . brazil has a high rate of covid-19 transmission. within 15 days, its number of cases had doubled, which translated to 500,000 new cases 9 . the heterogeneity and extensiveness show a burdensome scenario within the decision-making process and the need for protective measures. social inequalities enhance the necessity of deep analysis prior to easing restrictions based on intensive care units, infrastructure, and infection rates presented in section 3. for instance, the north region required significant medical support and structure in order to prevent a worse collapse in the health system. the northeast also showed high lethality and death rates, mainly in ceará and pernambuco. são paulo and rio de janeiro appear in almost all covid-19 analysis indicator rankings. both states represent the main economic poles in the country, and the high density of people in both areas highlights the importance of continuous tracking and testing. the brazilian government does not seem to be learning lessons from other countries, such as those referenced in section 3.1. as previously mentioned, all of them, except for the united states, only eased restrictions after intensive tracking, testing, and a descending curve in the number of daily cases was shown. são paulo and rio de janeiro, along with other states in brazil, do not follow the same approach (see figure 3a ). in addition, the number of active cases is still high, along with all other indicator analyses concerning each state. this is an urgent issue and must be addressed in all public spheres so that we can improve our response to the pandemic. in public health, prevention is always the least costly option, especially in this case, where an individual's response to the infection could be death. supported by the quantitative information in figure 2b demonstrating that brazil is expected to overtake the us in total number of cases (proportionally by population size), the current low isolation rates, low population testing percentage with consequently high under detection, high daily cases, and death rates all suggest that brazil has eased its restrictions prematurely and may face severe consequences in the near future as a result, such as becoming the next global epicenter of the pandemic. coronavirus cases [internet]. worldometers covid-19 cases in brazil surge to 330,890 ranking it as second place to america worldwide coronavírus brasil [internet]. brazilian government covid-19 lota hospitais e gera colapso funerário em belém demand for hospitalization services for covid-19 patients in brazil brazil loses second health minister in less than a month as covid-19 deaths rise [internet]. the guardian sob vaias e frases de apoio, bolsonaro come cachorro-quente em brasília doria anuncia flexibilização gradual da quarentena em são paulo agência brasil an interactive web-based dashboard to track covid-19 in real time a systematic review of covid-19 epidemiology based on current evidence science forum: sars-cov-2 (covid-19) by the numbers coronavirus disease (covid-19) -statistics and research epidemiologia clínica: elementos essenciais, artmed the deadly coronaviruses: the 2003 sars pandemic and the 2020 novel coronavirus epidemic in china the state council information office -the people's republic of china. full text: fighting covid-19: china in action asia may have been right about coronavirus and face masks, and the rest of the world is coming around life after lockdown: how china went back to work zealand's first covid cases in 24 days came from uk how new zealand's 'eliminate' strategy brought new coronavirus cases down to zero new zealand's prime minister may be the most effective leader on the planet coronavirus: aucklanders have to scan qr code to enter council buildings more covid-19 lockdown restrictions to be eased in new zealand south korea is relying on technology to contain covid-19, including measures that would break privacy laws in the us -and so far, it's working south korea's health minister on how his country is beating coronavirus without a lockdown how germany contained the coronavirus oversupply of hospital beds helps germany to fight virus italy's virus shutdown came too late. what happens now? learning from the italian experience in coping with covid-19 wikipedia contributors. brazil -wikipedia, the free encyclopedia com saúde em colapso, governo do amazonas usará contêineres frigoríficos para mortos do coronavírus governador do am escreve à onu e pede ajuda contra covid-19 na amazônia [internet]. uol notícias com necrotério lotado, corpos se acumulam em corredor de hospital no rj we thank the university of são paulo for technical support. the study did not require ethical approval since it is a descriptive study and there are no experiments involving humans. the authors declare that there is no conflict of interest. conception and design of the study, performed the computations, performed the analysis, wrote the paper; 7/8 ic: conception and design of the study, performed the computations, performed the analysis, wrote the paper; escf: performed the analysis, wrote the paper, reviewed the paper; fbj: interpretation of data, drafted the article, wrote the paper, reviewed the data; fab: model of data server, drafted the article, wrote the paper, reviewed the data; tlms: wrote the paper, reviewed the data; llo: wrote the paper, reviewed the paper; vcl: model of data server, drafted the article, wrote the paper, reviewed the data; nsbm: wrote the paper, reviewed the paper; da: conception and design of the study, final approval of the version to be submitted. key: cord-268296-w0i7rhru authors: barros, eliana nogueira castro de; cintra, otavio; rossetto, erika; freitas, laís; colindres, romulo title: patterns of influenza b circulation in brazil and its relevance to seasonal vaccine composition() date: 2015-11-25 journal: braz j infect dis doi: 10.1016/j.bjid.2015.09.009 sha: doc_id: 268296 cord_uid: w0i7rhru data on the burden of disease and circulation patterns of influenza b lineages for brazil are limited. this review aims to describe the pattern of influenza b occurrence in brazil to have a better understanding of its epidemiology and its relevance when considering seasonal influenza vaccine composition. a review of the data including analysis of international and local surveillance data as well as information from online search of databases using medical subject headings terms in conjunction with screening of abstracts from scientific events was performed. based on international epidemiologic surveillance data, moderate levels of influenza b disease (19%; 2006–2014) were observed. of these nine years, it was possible to compare data from three years (2007, 2008 and 2013) which have information on the circulating influenza b lineage. co-circulation of influenza b lineages was observed in all these three influenza seasons, of which, during one season, a high degree of mismatch between the vaccine lineage and the predominant circulating lineage (91.4% [2013]) was observed. local surveillance data reveal a distinct and dynamic distribution of respiratory viruses over the years. data from published literature and abstracts show that influenza b is a significant cause of disease with an unpredictable circulation pattern and showing trends indicating reemergence of the b/victoria lineage. the abstracts report notable levels of co-circulation of both influenza b lineages (2000–2013). mismatch between the southern hemisphere vaccine and the most prevalent circulating viruses in brazil were observed in five influenza seasons. the evidence on co-circulation of two influenza b lineages and mismatched seasons in brazil indicates the benefit of quadrivalent influenza vaccines in conferring broader seasonal influenza protection. additionally, improving influenza surveillance platforms in brazil is important for monitoring disease trends and the impact of introducing seasonal influenza vaccination. influenza is a highly infectious acute viral illness resulting in significant morbidity as well as healthcare resource utilization. in healthy individuals influenza is generally self-limiting, but can often cause complications. 1, 2 there are 3 types of seasonal influenza viruses -a, b, and c. influenza a causes moderate to severe illness and affects individuals of all age groups. influenza b can cause disease of similar severity as influenza a, and even though the morbidity is higher in children, all age groups can be affected. 3, 4 the influenza b virus is more stable than influenza a, with less antigenic drift and consequent immunologic stability, and does not undergo the process of antigenic shift. influenza c is rarely reported as a cause of human illness, probably because most cases are subclinical. 5 both influenza a and b cause annual epidemics worldwide and are estimated to result in 3-5 million cases of severe illness, and 250,000-500,000 deaths. 6 influenza vaccination is the most important prophylactic intervention against infection. until the 2012-2013 influenza season, use of trivalent inactivated influenza vaccines, containing two influenza a strains (a[h1n1] and a[h3n2]) and one influenza b lineage (b/yamagata or b/victoria) was recommended for use in immunization programs by the world health organization (who). 6 as influenza viruses undergo frequent changes in their surface antigens, new influenza vaccines are designed annually to match the circulating virus subtype expected for the next influenza season. 7 the selection of the influenza b lineage is considered critical in determining the effectiveness of vaccination programs. 7 unfortunately, the correct prediction of the predominating circulating b lineage is quite difficult, often leading to inaccuracies in prediction, causing a mismatch between the recommended vaccine lineage and the circulating influenza b lineage. prior studies have raised concerns that mismatches can result in lower vaccine effectiveness, due to the absence of cross-protection between antigenically distinct influenza b lineages, leading to more influenza cases, 8, 9 and an increase in influenzarelated medical resource utilization and costs. 2, 10 in addition to this, matias et al. 11 have found that influenza b-associated mortality could serve as a surrogate marker of disease severity. in the latin america and caribbean region, seasonal influenza causes high morbidity placing a substantial economic burden on healthcare systems and society. 12 data on the burden of influenza disease for brazil are limited, most likely due to underreporting. 12 between 2000 and 2008, data from the influenza surveillance system in brazil revealed that influenza-like illness (ili) led to a total of 4.39-16.92% of hospital consultations, and in 2008, of all positive reported influenza cases, 43.29% (95% ci: 37.59-49.13) were influenza b. 12 the ministry of health (moh, "ministério da saúde") of brazil promotes annual national influenza vaccination campaigns. over the years, there has been a gradual expansion of the recommended groups for annual influenza immunization in brazil. 13 since 1999, influenza vaccination was introduced for elderly people aged above 65 years and other groups vulnerable to complications (patients with co-morbidities). in the year 2000, individuals 60 years or older were included for vaccination. 14, 15 during 2011-2012, in addition to elderly people, vaccination was extended to children aged six months to those aged below two years, pregnant women, healthcare professionals, and indigenous people. in 2013, women after child birth, individuals with chronic disease and transplant, and individuals in detention facilities were included for annual influenza vaccination. in 2014, children aged 2-4 years were also included in the recommended target at-risk groups for vaccination. the information system of national immunization program for brazil ("programa nacional de imunizaç ão") 13 reported that across all target vaccination groups, overall mean vaccination coverage of 86.8% was reached in 2014. 13 during all influenza vaccination campaigns in brazil, trivalent vaccines were used according to who recommended vaccine composition for south hemisphere. 16 although high vaccination coverage levels have been reached in these target vaccination groups, little is known about the effectiveness of vaccination programs in brazil. 14, 17 a number of factors, in particular vaccine coverage, is known to influence the effectiveness of influenza vaccination programs. however, the brazilian moh data shows vaccine coverage to be high in almost all years since the introduction of vaccination. importantly, the extent to which the vaccine recommended influenza b virus lineage matches the influenza virus lineage circulating in the population during an influenza season is known to impact the effectiveness of seasonal influenza vaccination programs. 14 data on laboratory surveillance of the influenza b virus in brazil are limited, specifically data on the burden of disease and circulation patterns of influenza b lineages. the present integrative review of publicly available data aims to consolidate findings on the pattern of influenza b occurrence in brazil to have a better understanding of influenza b epidemiology and its relevance to seasonal vaccine composition. different sources were used to retrieve information on epidemiological surveillance. we referred to international data sources to check who recommendations on the vaccine composition in the southern hemisphere, 18 and information on circulating influenza lineages for brazil, the south america region and globally from the who/flunet database which provides data through its network -global influenza surveillance and response system (gisrs) laboratories. 19 consolidation of available national epidemiological information on influenza in the epidemiological bulletins of the brazilian moh was also performed. bulletins available from 2009 to epidemiological week 35 of 2014 were considered. 15 in brazil, two types of surveillance exist: sentinel surveillance of ili and universal severe acute respiratory syndrome (sars) surveillance. ili is defined as fever followed by cough or sore throat and symptoms onset within the last seven days. sars is defined as fever followed by cough or sore throat and experiencing dyspnea, requiring hospitalization. oxygen saturation levels lower than 95%, respiratory distress, or respiratory rate increase, are also considered in sars. the sentinel ili surveillance, which has a network of units distributed throughout the country's geographic regions, is used in the identification and characterization of circulating respiratory viruses in viral isolations. the universal sars surveillance, which was implemented post-identification of the influenza a(h1n1) 2009 pandemic strain (pdm09), monitors hospitalized cases and deaths. in both systems, data are collected by means of standardized forms and entered into the online information systems: influenza epidemiological surveillance system called sivep-gripe for ili cases, and the national information system for notifiable diseases known as sinan influenza web for sars cases. results from tests performed at the 27 public health central laboratories ("laboratórios centrais de saúde pública, lacen") are routinely included in these systems. the diagnostic kits currently available identify the influenza a(h1n1)pdm09 viral strain (determined by who), influenza a(h3n2), influenza a not subtyped, and influenza b virus. the antigenic characterization of the circulating influenza virus lineage is performed by three laboratories in brazil ("instituto evandro chagas" -pará, "instituto adolfo lutz", são paulo and "instituto oswaldo cruz", rio de janeiro). these laboratories are part of a network of 140 national influenza centers acknowledged by who as members of the gisrs. an integrative literature review was performed using online database tools such as pubmed/medline, lilacs and scielo. searches on online databases were conducted using the following search strategy built for the pubmed database (via medical subject headings [mesh] controlled vocabulary) and adjusted for other databases according to their specificities: "(((((influenza [title/abstract]) or influenzae)) or ((orthomyxoviridae [mesh major topic]) or influenza, human [mesh major topic]))) and brazil". studies on influenza b, with brazil as the place of study and those with virological influenza b information were considered. articles published between 2007 and 2014 were considered and a language constraint was not applied. articles and abstracts with general influenza reports or without subtyping (a or b) were not included. one reviewer screened titles and abstracts for relevance, as the defined inclusion criteria were restrictive. an additional research was conducted in abstracts of the annals of scientific events related to the area of research. a total of 10 events were considered. 20-29 all authors agreed with the selected publications. data on viral lineage isolation and characterization, vaccination campaign, viral lineage surveillance and strain match-mismatch from different sources were collected and consolidated. statistical analysis was not performed, and thus all data are descriptive. the pattern of hospitalized sars cases from the universal sars surveillance showed that in 2013, although influenza a(h1n1)pdm09 was predominant, 22.5% of sars cases positive for influenza (1337/5935, with 85 deaths) were caused by the influenza b virus. regional variation was observed between the regions -south region (29%) and north region (12%). in 2014 (up to epidemiological week 35) 6% of sars cases positive for influenza (75/1307, with 9 deaths) were caused by the influenza b virus (table 1) . a total of 722 articles were identified, of which 602 articles were excluded after the review of titles as they were related to influenza other than influenza b. subsequent to the screening of titles, abstracts of the 120 potentially relevant articles were reviewed and, as a result, 108 articles were excluded when the eligibility criteria were not met (fig. 2) . in all, 12 articles presenting evidence on influenza b virus circulation in brazil for the years 1996-2013 were included. [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] details for each of the studies are shown in supplementary file 1. two studies detailed characteristics of an influenza outbreak in february 2012 on cruise ships. 32, 35 fernandes et al. 35 reported findings from the first influenza outbreak detected by brazilian public health authorities in a vessel cruising in south america. of 11 hospitalized cases of acute respiratory illness, there were six cases with influenza b virus detected in the nasopharyngeal isolates. 35 in another study by borborema et al. 32 , it was shown that the influenza b virus was the cause of the outbreak (detected in seven individuals with respiratory illness). other reports from the online literature review were primarily from retrospective descriptive studies. freitas 36 showed that influenza b was attributable to moderate levels of disease during 2000 and 2010 (3-17%), and its occurrence was notable in the south and central-west regions. paiva et al. 37 confirmed the reemergence of the b/victoria viruses in são paulo, brazil, during the years 1996-2012. in table 2 , based on who/flunet reports, consolidated annual data on the lineages that were part of the vaccine, the proportion of predominant circulating lineages and the proportion of lineage mismatch is shown for south america and brazil. data for brazil was available for nine years; of these, it was only possible to compare data from three years (2007, 2008 and 2013) which have information available on the circulating influenza b virus lineage. in brazil, co-circulation of both influenza b lineages was detected in all these three influenza seasons, and a high level of mismatch (91.4%) was observed in one year (2013) ( table 2 ). in the same year for south america 52.0% (2013) of mismatch was observed. that in 2013, a high degree of mismatch between the vaccine and the predominating circulating lineage (91.4%) occurred, and during the other two influenza seasons, a partial mismatch was reported. the three reviewed abstracts, which specifically report findings on influenza b mismatch, corroborate this unpredictable behavior of influenza b disease in brazil for many other seasons for which data were not available in the international epidemiological surveillance data. significant levels of co-circulation of both influenza b lineages (b/victoria and b/yamagata) and lineage mismatch between the vaccine and circulating lineage was reported for brazil in five influenza seasons (2002, 2005, 2008, 2010, and 2013) . [42] [43] [44] previous studies suggest that even with a partial mismatch over the years, due to the unpredictability of influenza b lineage circulation, the disease burden (in terms of clinical cases, hospitalizations and health care resource utilization) and societal burden can be considerable. 2, 9 for example, a mismatch in the 2007-2008 influenza season in the united states was estimated to have costed health care providers and society well over $100 million and $1 billion, respectively. 45 in another study conducted in taiwan, it was reported that an epidemic predominated by influenza b/yamagata lineage occurred during the 2011-2012 season during which the trivalent influenza vaccine contained influenza b/victoria lineage. expectedly, the morbidity and mortality of this vaccine mismatched epidemic was substantial (influenza b: 60.7% and 66.9% of confirmed influenza cases and deaths, respectively; 87.2% of samples showed the presence of vaccine opposite lineage). 46 surveillance data on the age distribution of influenza cases is available only for 2013. this data showed that influenza b virus was predominantly observed in younger individuals aged 5-29 years, with the highest proportions in children aged 5-9 years and 10-19 years. even though this observation was restricted to only one year with 90% mismatch it is in line with previous reports wherein influenza b has been reported to affect more schoolchildren and the appearance of the new b lineage reinforced this pattern. 4 an implication of this finding is that children and adolescents might benefit the most from the addition of a second influenza b lineage to the seasonal influenza vaccine. moreover, it could be useful for the entire population as it is widely considered that vaccinating children can reduce influenza illness in family members and other susceptible populations in the community by reducing the risk of exposure and subsequent influenza infection and related complications. 47 11 that influenza b-associated mortality could potentially be a valid indication of disease severity. thus the evidence presented here for one year underscores the importance of a universal influenza vaccination strategy compared to targeted immunization as universal immunization at high vaccine coverage levels could potentially interrupt transmission reducing the occurrence of outbreaks and severe disease. our literature review confirms the re-emergence of b/victoria lineage in brazil during the years 2000-2002. these data are in line with that of motta et al. 48 which shows the re-emergence of the victoria-lineage viruses in the northern hemisphere and in the south and south east regions of brazil where previously the b/yamagata lineage was the predominating circulating lineage and the vaccine recommended lineage. other studies confirm that the b/yamagata was the major circulating lineage until the 1980s, when b/victoria lineage viruses appeared; since then, drift variants of both influenza b lineages have been co-circulating worldwide. 49, 50 as influenza b viruses can co-circulate during an epidemic allowing the re-emergence of old lineages due to re-assortment between the different strains, 4,48 there is a need to improve influenza laboratory-based surveillance in brazil. importantly these data also highlight the unpredictability of influenza b circulation, making it difficult to consistently predict which b lineage will predominate during a given influenza season. due to the little cross-protection conferred between the two antigenically distinct influenza b lineages, a vaccine lineage mismatch with the circulating lineage could result in additional burden in terms of health care resource utilization and can adversely impact the society. this burden could, in particular, be substantial during an outbreak. to avoid this additional burden, a plausible option would be to switch from the use of trivalent influenza vaccines to quadrivalent vaccines in national campaigns. 51 quadrivalent influenza vaccines are expected to offer broader protection against influenza b disease. the who recently updated recommendations beginning with the 2013-2014 influenza, now recommending the use of a quadrivalent vaccine composition with the addition of a second influenza b lineage as well as the two influenza a strains and one influenza b lineage contained in the trivalent vaccines. 6, 52 some limitations of this review require consideration. besides the inherent limitations of each of the studies included in the literature search and abstracts, there are other important limitations. statistical and quality analysis of the articles was not performed. also, the interpretation of data is constrained by the gaps in laboratory surveillance in which there were no influenza b data available for many years with respect to age, severity, and seasonality. as we present data over many years through which the surveillance system has gradually improved, the number of positive samples is still small, and the more recent years are likely to be overrepresented. additionally, sentinel surveillance data cannot be truly representative for the whole population as the system of sentinel units involves different levels of care. moreover, there is no standard protocol for patient selection for sample collection which may have led to a selection bias of certain age groups. despite these limitations, the surveillance system for influenza and other respiratory viruses which has improved over the years has proven useful to describe influenza b circulation patterns for brazil and demonstrate that influenza b epidemiology is changing in line with observations reported from other countries. 4 influenza surveillance systems, and laboratory-based and epidemiological studies of influenza b in brazil, while limited, have improved over the years. there is a need to strengthen and extend influenza surveillance for influenza b sample subtyping to determine the behavior pattern of influenza b lineages. the findings from this integrative data review provide evidence of the unpredictable nature of influenza b circulation in brazil, the increasing frequency of co-circulation of both influenza b lineages, and mismatch between the circulating influenza b lineage and the composition of the seasonal influenza vaccine for the region. this data is suggestive of the additional benefit that quadrivalent influenza vaccines, containing both influenza b lineages (b/yamagata and b/victoria), could offer over the use of the currently available trivalent vaccines for the prevention of seasonal influenza in brazil. all authors participated to the conception/design of the review, performed or supervised the analysis, and interpreted the data. otavio cintra, eliana nogueira castro de barros, laís freitas and erika rossetto collected or assembled the data. erika rossetto wrote the preliminary report of the review findings. all authors read and approved the final manuscript. eliana nogueira castro de barros, otavio cintra and romulo colindres are employees of the gsk group of companies. romulo colindres and otavio cintra report ownership of stock options and/or restricted shares. laís freitas reports that she is working for gsk vaccines, but is employed by shift de gestão em serviç os. erika rossetto has no conflict of interest. population-based study on incidence, risk factors, clinical complications and drug utilisation associated with influenza in the united kingdom influenza-related health care utilization and productivity losses during seasons with and without a match between the seasonal and vaccine virus b lineage comparison of influenza a and influenza b virus infection in hospitalized children editorial commentary: changing epidemiology of influenza b virus public health foundation influenza (seasonal) world health organization.who position paper: influenza vaccines estimating vaccine effectiveness against laboratory-confirmed influenza using a sentinel physician network: results from the 2005-2006 season of dual a and b vaccine mismatch in canada influenza vaccine: the challenge of antigenic drift impact of influenza b lineage-level mismatch between trivalent seasonal influenza vaccines and circulating viruses estimates of mortality attributable to influenza and rsv in the united states during 1997-2009 by influenza type or subtype, age, cause of death, and risk status. influenza other respir viruses burden of influenza in latin america and the caribbean: a systematic review and meta-analysis. influenza other respir viruses ministério da saúde departamento de informática do sus (datasus) effectiveness of the brazilian influenza vaccination policy, a systematic review ecological study on mortality from influenza and pneumonia before and after influenza vaccination in the northeast and south of brazil. cadernos de saúde pública world health organization. who recommendations on the composition of influenza virus vaccines. influenza ministério da saúde secretaria de vigilância em saúde. oordenação geral de doenças transmissíveis world health organization. influenza vaccine viruses and reagents european society for paediatric infectious diseases 24. international congress on infectious diseases options for the control of influenza world society for pediatric infectious diseases patterns of influenza infections among different risk groups in brazil acute respiratory infection and influenza-like illness viral etiologies in brazilian adults molecular characterization of influenza b virus outbreak on a cruise ship in brazil 2012 applications of a duplex reverse transcription polymerase chain reaction and direct immunofluorescence assay in comparison with virus isolation for detection of influenza a and b impact of respiratory infections by influenza viruses a and b in pediatrics patients from federal university of parana, brazil influenza b outbreak on a cruise ship off the sao paulo coast, brazil sentinel surveillance of influenza and other respiratory viruses, brazil evolutionary pattern of reemerging influenza b/victoria lineage viruses in sao paulo, brazil, 1996-2012: implications for vaccine composition strategy etiologia viral das infecç ões respiratórias agudas em população pediátrica no instituto fernandes figueira/fiocruz/rj análise filogenética e padronização da técnica de eletroforese em gel com gradientes desnaturantes (dgge) para caracterização das linhagens do vírus influenza b identificadas durante as epidemias de vigilância de oito vírus respiratórios em amostras clínicas de pacientes pediátricos no sudeste do brasil the epidemiology and antigenic characterization of influenza viruses isolated in curitiba, south brazil mismatch between vaccine strains and circulating influenza b viruses in different regions of brazil: 2001-2013. options for the control of influenza. cape town influenza virus surveillance conducted by the institute adolfo lutz influenza b circulation during twelve influenza seasons (2001-2013) in a tertiary hospital in sao paulo, brazil. options for the control of influenza. cape town the economic value of a quadrivalent versus trivalent influenza vaccine surveillance and vaccine effectiveness of an influenza epidemic predominated by vaccine-mismatched influenza b/yamagata-lineage viruses in taiwan, 2011-12 season assessing optimal target populations for influenza vaccination programmes: an evidence synthesis and modelling study the reappearance of victoria lineage influenza b virus in brazil, antigenic and molecular analysis genetic analysis and evaluation of the reassortment of influenza b viruses isolated in taiwan during the reappearance and global spread of variants of influenza b/victoria/2/87 lineage viruses in the world health organization. influenza recommended composition of influenza virus vaccines for use in the 2015 southern hemisphere influenza season the authors would like to thank andreza madeira macario (epidemiologist to inovatec) for intellectual contribution to the study, amrita ostawal for medical writing services (consultant publications writer to gsk vaccines) and bruno dumont (business & decision life sciences on behalf of gsk vaccines) for editorial assistance and publication coordination. supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/ j.bjid.2015.09.009. r e f e r e n c e s key: cord-340942-oatf59k0 authors: magalhães, jurandy júnior ferraz de; mendes, renata pessoa germano; silva, caroline targino alves da; silva, severino jefferson ribeiro da; guarines, klarissa miranda; pena, lindomar title: epidemiological and clinical characteristics of the first 557 successive patients with covid-19 in pernambuco state, northeast brazil date: 2020-09-21 journal: travel med infect dis doi: 10.1016/j.tmaid.2020.101884 sha: doc_id: 340942 cord_uid: oatf59k0 background: south america is the current epicenter of covid-19 pandemic. yet, the epidemiological and clinical features of the disease have not been described in brazil, the third most affected country in the world. methods: in this retrospective study, we describe the demographics, epidemiology and clinical features of the first 557 consecutive patients positive for sars-cov-2 living in pernambuco state, northeast brazil. results: the first covid-19 cases occurred in the high income population. the age of infected patients ranged from 27 days to 97 years with a median of 47 years. the ratio of males to female in the sars-cov-2-infected group was 0.83:1. the most common symptom was cough (74.51%), followed by fever (66.79%), dyspnea (56.01%), sore throat (28.19%) and o(2) saturation <95% (24.42%). 86.44% of the lethal cases were patients older than 51 years. the median time from illness onset to diagnosis was 4.0 days (range 0–39 days) severe patients diagnosed after 14 days of symptoms onset had higher viral load than patients with mild disease. conclusions: our study provides important information about covid-19 in the tropics and will assist physicians and health officials to face the current pandemics as sars-cov-2 continues to spread in the human population. in late december 2019, a cluster of severe pneumonia cases of unknown origin was reported in wuhan, hubei province, china [1] . the disease, later named coronavirus disease 2019 (covid19) , was caused by a novel coronavirus identified as severe acute respiratory syndrome coronavirus 2 (sars-cov-2) [2, 3] . similar to other highly pathogenic coronaviruses (covs -sars-cov and middle east respiratory syndrome cov (mers-cov), sars-cov-2 belongs to β genus within the coronaviridae family and emerged from bats. the rapid spread of sars-cov-2 around the world caused the world health organization (who) to declared covid-19 as a pandemic on march 11, 2020 [4] . china was the first epicenter of pandemic, followed by europe, the usa, and now south america. on february 26, 2020, brazil reported the first case in latin america in a são paulo patient returning home after a work trip to italy from february 9th to 21st. the patient had a mild respiratory disease characterized by coryza, dry cough, and sore throat [5] [6] [7] . since then, the number of covid-19 cases in brazil has increased steadily and the country has become the third most affected in the world after the usa and india. given the paucity of diagnostic tests in developing countries, the actual incidence of covid-19 in brazil is heavily underestimated. for instance, while the usa has done 282,114 tests per million inhabitants, brazil has performed only 68,143 tests/million people (https://www.worldometers. info/coronavirus/). as of september 15, 2020, brazil has confirmed 4.3 million covid-19 cases and 132,297 deaths (https://www.wor ldometers.info/coronavirus/). pernambuco is one of the most affected state in brazil with 137.869 cases and 7914 deaths [8] . the emergence of sars-cov-2 caused a profound change in the global scenario and recruited public health authorities and research groups from different parts of the world to fill knowledge gaps in the biology and pathogenesis of this devastating pathogen. although the epidemiological and clinical presentation of covid-19 has been well documented in several countries of the northern hemisphere, information regarding the clinical features of covid-19 in latin america, especially in brazil, remains scarce and limited. thus, an updated analysis of cases could help to significantly improve our knowledge and consequently provide insights into covid-19 in this region of the planet, given its unique climate, social dynamics, population genetics and political scenario [9] . here, we describe for the first time the clinical, epidemiological and demographic features of the first 557 laboratory-confirmed covid-19 cases in pernambuco state, northeast brazil, who were diagnosed between march 12 and april 22, 2020. a total of 557 patients living in pernambuco state with a positive sars-cov-2 nucleic acid test were included in this study. patients were considered to have confirmed covid-19 infection if they had at least one positive rt-qpcr test for sars-cov-2. this study was approved by the upe institutional review board under protocol caae: 27607619.0.0000.5207 and was performed in accordance with relevant guidelines e regulations, including the brazilian national health council (cns) resolution 466/2012. the requirement for informed consent study was waived based on the nature of this observational retrospective study, in which patient identifying information were kept confidential. patient epidemiological information, demographic and clinical characteristics, including medical history, signs and symptoms, laboratory findings, underlying co-morbidities, and date of disease onset were obtained from electronic medical records of the pernambuco central public health laboratory (lacen) and analyzed. patient outcome data were obtained from march 12 to 22 april 2020, the final date of followup. all covid-19 patients enrolled in this study were diagnosed according to world health organization interim guidance [10] . laboratory confirmation was performed at the pernambuco lacen, which is one of the designated laboratories for the diagnosis of sars-cov-2 in this state. nasopharyngeal and oropharyngeal swabs were collected from patients presenting respiratory signs of disease compatible with covid-19. after sample collection, viral rna was extracted using the reliaprep viral tna miniprep system kit (promega, madison, wi, usa), according to the manufacturers' instructions and the rna was used for rt-qpcr following the protocol for sars-cov-2 detection established by corman and coworkers [11] . spatial analysis were done by georeferencing only the addresses of individuals residing in recife (n = 306), capital of the state of pernambuco and city with the largest number of confirmed cases of covid-19 at the time of this analysis. for that, the qgis software (https://qgis. org/en/site/) was used to plot home addresses and the kernel density estimation method was applied to identify the neighborhoods with the highest concentration of covid-19 cases. we also calculated the incidence of infection in the neighborhoods and that concentration of cases were displayed on a heat map. the location of the georeferenced addresses was produced on a scale of 1:215,000, which means that on the map, the location of the addresses presents an error of approximately 0.4 mm (40 m on the real scale). therefore, the addresses of individuals are located in an area of approximately 2500 m 2 . as recife is an urbanized city, ethical concerns are not applicable because it is not possible to verify the exact location of each residence. the cartographic base used was acquired in shapefile format at the website of the brazilian institute of geography and statistics (ibge) in the geocentric reference system for the americas (sirgas) 2000. in addition, we built a graduated map with information on the income of households in the neighborhoods from the city of recife and we classified the neighborhoods based on the amount of minimum wages received to correlate the distribution of covid-19 cases within the different ranges of household income of the studied population. we used data on minimum wages and average monthly nominal income per household from the last brazilian census (http://censo2010.ibge.gov.br/). microsoft office excel (version 2010) was used to build a database with patient's information. data process and analysis were made using the graphpad prism version 6.0 for windows (graphpad software, la jolla, ca, usa). continuous variables were expressed as medians and interquartile ranges, as appropriate. categorical variables were summarized as counts and percentages. a chi-square test was used to investigate the level of association among variables. statistically significant differences were defined as p < 0.05. from 12 march to april 22, 2020, a total of 2772 suspected cases-1616 females (58.30%) and 1156 males (41.70%) -were collected and tested for sars-cov-2 at the pernambuco lacen by rt-qpcr. from total cases, 557 (20.09%) were positive for sars-cov-2. these were the first covid-19 cases reported in the state. fig. 1 illustrates the epidemic distribution in pernambuco state. the highest number of cases (n = 304, 54.58%) occurred in the city of recife, capital of pernambuco, followed by the metropolitan cities jaboatão dos guararapes (n = 43, 7.72%), olinda (n = 43, 7.72%), paulista (n = 30, 5.39%), são lourenço da mata (n = 23, 4.13%), and camaragibe (n = 16, 2.87%). the first 304 cases of covid-19 in recife were georeferenced using the kernal density estimate. the highest case numbers were concentrated in the neighborhoods of casa amarela, parnamirim, rosarinho, encruzilhada, espinheiro, graças, torre, madalena, and boa viagem (fig. 1a ). the rosarinho neighborhood had the highest incidence of covid-19 (12.26/10 4 inhabitants) and also had the highest number of cases per square kilometer (20/km 2 ), while the guabiraba neighborhood had the lowest incidence (1.58/10 4 inhabitants) and a lower number of cases per square kilometer (0.02/km 2 ). regarding the distribution of covid-19 cases in the different household income ranges (fig. 1b) , we found that sars-cov-2 infections occurred in neighborhoods with greater purchasing power. of the nine neighborhoods highlighted on the heat map, seven had households with earnings greater than 10 minimum wages, demonstrating that the first covid-19 cases in pernambuco target the high income population. fig. 1a shows the spatial distribution of covid-19 cases in recife, pernambuco capital as heat map. the kernel density estimate was used to show the areas with the highest concentration of cases associated with the incidence of the disease in some neighborhoods. fig. 1b shows a graduated map with information on the average nominal monthly household income converted into the amount of minimum wages. fig. 1c shows the cities with covid-19 positive cases in the state of pernambuco. pernambuco was notified on march 12, 2010. during the first week, 29 (5.20%) cases and 2 (3.38%) deaths were registered. the fourth week (from 7 to 14 april) registered the greatest increase in the number of cases and deaths. a total of 354 (63.55%) cases and 29 (49.15%) deaths were recorded in that period, which corresponded to 501 (89.94%%) accumulated positive cases and 58 (98.30%) deaths. the age of sars-cov-2 infected patients ranged from 27 days to 97 years with a mean of 48.57 years and a median of 47 (interquartile range [iqr], 32 to 68). the ratio of males to female in the sars-cov-2infected group was 0.83:1 (45.42% males/54.58% females; chi-square test, p = 0.46), showing a slight higher incidence in females than males. the highest number of cases occurred in patients aged 31-40 years old (n = 128, 22.98%), followed by the 41-50 years age group (n = 121, 21.72%), and the group embracing patients from 51 to 60 years old (n = 101, 18.13%). during the study period, a total of 59 deaths occurred. among these, 51 (86.44%) were patients older than 51 years. although the incidence was more elevated in females, the number of deaths tended to be higher in males (55.93% versus 44.06%), despite the difference not reaching statistical significance (chi-square test, p = 0.87). the mean age of deceased patients was 66.06 years and the median was 65 (interquartile range, 51.5-82.5). the highest mortality rate was observed in patients in the 61-70 years age group (n = 18, 30.50%), followed by the 51 to 60 age group (n = 11, 18.64%) (fig. 2b) . fig. 3a summarizes the main symptoms presented at the time of patient notification. the most common symptom was cough (n = 415, 74.51%), followed by fever (n = 372, 66.79%), dyspnea (n = 312, 56.01%), sore throat (n = 157, 28.19%) and o 2 saturation <95% (n = 136, 24.42%). some patients also presented myalgia (n = 28, 5.03%), headache (n = 24, 4.31%), running nose (n = 20, 3.59%), diarrhea (n = 17, 3.05%), and vomiting (n = 9, 1.62%). fig. 3b shows the symptoms according to age groups. the most prevalent symptom in patients aged less than 20 years old were fever, cough and dyspnea. in addition to these symptoms, sore throat, myalgia, headache, diarrhea, vomiting and runny nose were more common in people aged over 20 years old. the highest rate of patients with saturation <95% was found in individuals aged over 61 years. the average time from the symptoms onset to notification date was 4.85 days while among deceased patients this number was 4.52 days. we next sought to investigate the virus shedding pattern in patients at the time of diagnosis. information on the quantitation cycle (cq) was available for 388 patients. the cq value was used to estimate the viral load of patient's nasopharyngeal specimens, in which lower cq values indicate higher amount of virus. the median cq of the patients was 26.3 (sd = 5,7) and ranged from 13.3 to 39.3. to evaluate sars-cov-2 shedding patterns in this cohort, the data were further stratified according to the day of symptoms onset at the time of sampling. the median time from illness onset to diagnosis was 4.0 days (sd = 4,7), with a range of 0-39 days (fig. 4a) . we then compared the viral load of severe cases (patients that were admitted to icu and the ones that have died) with mild cases at different days since symptoms onset (fig. 4b) . there was no statistically significant difference in viral load at the time of diagnosis of patients with mild or severe covid-19 up to 14 days of symptoms onset. however, patients with severe disease diagnosed after 14 days of symptoms onset had higher viral load than patients with mild disease (p = 0.0218). the clinical evolution of patients reported up to the date of notification (april 22nd, 2020) indicated that 50.63% (282/557) were in selfisolation, 26.93% (150/557) were in general hospital wards, 5.38% (30/ 557) required intensive care unit (icu) care, 6.46% (36/557) fully recovered from the disease and 10.59% (59/557) of the patients evolved to death (table 1) . information on comorbidities was available to 116 patients. a total of 72.27% of the patients reported comorbidities. the most common comorbidity was arterial hypertension (26.72%), followed by diabetes mellitus (16.38%), cardiovascular diseases (13.79%), asthma (6.89%), lung disease (4.31%), obesity (2.59%), and kidney disease (0.87%) (fig. 5) . brazil remains the third most affected country after the usa and india. after its initial detection on february 26, 2020, sars-cov-2 has spread to all its 26 states and the federal district. yet, the epidemiological and clinical profile of covid-19 in brazil has not been reported in the literature. here, we described for the first time the epidemiological and clinical characteristics of the first 557 consecutive patients diagnosed with sars-cov-2 in the state of pernambuco between 12 march and april 22, 2020. the first patients diagnosed with sars-cov-2 in pernambuco were an elderly couple (71-year-old man and 66-yearold woman) returning from rome, italy on 29 february and whose diagnostic was confirmed on 12 march. the couple lived in the boa viagem, a high-income neighborhood located in the southern region of the city (fig. 1) . this couple had returned from a trip to italy and sought medical treatment on march 5, 2020, when italy already had 3858 confirmed cases of covid-19 (who). on march 17, pernambuco reported local transmission of sars-cov-2 for the first time and since then the number of new cases has increased steadily first in the metropolitan area and then spreading to inland cities. the state capital, recife had the highest number of covid-19 cases in the study period. as shown in fig. 1b , the first sars-cov-2 cases were concentrated in neighborhoods with a higher nominal monthly household income, such as the rosarinho, espinheiro, and boa viagem neighborhoods that had average earnings above 10 brazilian minimum wages. our data is in agreement with a study done in rio de janeiro, brazil in which the highest rates of covid-19 were observed in the wealthiest regions [12] . despite the epidemiological evidence and the first detection of sars-cov-2 in the boa viagem neighborhood with subsequent spread mainly to high income neighborhoods, it is not possible to say with certainty that sars-cov-2 infections in pernambuco started from these places. for that, robust phylogeography analyses based on sars-cov-2 genomic sequences from these patients would be necessary to definitely understand the its transmission dynamics and associate it with clinical and epidemiological data. nevertheless, individuals with high household income are more likely to take costly international trips and are therefore expose themselves to the risk of acquiring an infection overseas. in fact, the index covid-19 case in brazil was diagnosed in são paulo in patient returning from a trip from italy. phylogenetic analyses of the first patients in são paulo coupled with travel history information confirmed multiple independent importations from italy and local spread during the initial stage of sars-cov-2 transmission in the country [13] . our results highlights the importance of emerging diseases strengthening programs and preventing people who have traveled to different locations in the world from returning to their countries without undergoing quarantine and testing upon return to their home country. the median age of the patients included in this study was 47 years (iqr 32 to 68), ranging from 27 days to 97 years. however, the median age of deceased patients was 65 years. in our study, only 14 cases (2,51% of total) were reported in patients aged less the 20 years, whereas a large proportion of cases (44,70% of total) were in patients aged 31-50 years old. lethal cases in this cohort were concentrated in patients older than 51 years, which accounted for 86.44% of total deaths. our data is in agreement with a study conducted by guan et al. where the median age of sars-cov-2 infected patients was 47 years (iqr: 35 to 58) and only 0.9% of patients were under 15 years old [14] . in another study carried out in china, the most affected patients were in the 50-59 years age group, whereas fatal cases were concentrated in the 70-79 years group [15] . in our study, a higher proportion of women sought medical attention upon suspecting of a respiratory disease (58.30% females and 41.70% males) and sars-cov-2 positivity was higher in female (54.58%) than males (45.42%). the data is in agreement with 102,646 cases of covid-19 cases reported in canada to date, in which 56% occurred in females [16] . this sex discrepancy in our studyt might be due to lifestyle behavior in which women are more likely to seek medical care at the first signs of disease than men. the covid-19 lethality in this study showed a higher tendency in males than females (55.93% versus 44.06%), although it not reached statistical significance. in general, the men to women ratio of covid-19 prevalence is the same, but men with covid-19 tend have higher risk of developing the severe forms of the disease and die from it [17, 18] . we found that cough, fever and dyspnea were the most common symptoms. the main symptoms showed in our study were also reported by others [19] [20] [21] [22] . wan et al., 2020 demonstrated that fever (88.9%) and cough (76.5%) were also the most common symptoms, however, dyspnea was present in only 13.3% of patients [23] . gastrointestinal manifestations were less prevalent. lower frequency of gastrointestinal symptoms is also shown in other studies [14, 20] . the virus shedding pattern in patients at the time of diagnosis was investigated in this study. our data demonstrated that the median time from symptoms onset to viral rna shedding was 4 days, ranging from 0 to 39 days. this data is in agreement with a study in wuhan in which the longest duration of viral shedding in survivors was 37 days [21] . comparison of the sars-cov-2 load of severe cases with mild cases at different days since symptoms onset did not find a statistically significant difference up to 14 days of symptoms onset, but lately diagnosed patients (after 14 days) had higher viral load than patients with mild disease (p = 0.0218). recently, liu and co-workers studied the viral dynamics in mild and severe cases of covid-19 and found that patients with severe disease had about 60 times higher viral load than that of mild cases [24] , irrespective of the day of symptoms onset. in this cohort, 10.59% of the patients died from covid-19. the high case-fatality rate may be overestimated in this cohort may be due scarcity of testing in brazil compared to developed countries. for instance, brazil has performed only 68,143 tests per million people, whereas this rate in developed countries is over 100 thousand per million inhabitants. as of september 15, 2020, the case-fatality rate of covid-19 is about 3.15%, with 936,651 deaths and 29,648,872 confirmed cases worldwide (https://www.worldometers.info/coronavir us/). a significant proportion of cases (72.27%) in this cohort reported comorbidities and arterial hypertension was the most common condition associated with covid-19 infection followed by diabetes mellitus. our findings is in accordance with a study investigating the first 1000 consecutive patients in new york [25] and also in other regions of the world [26] . sars-cov-2 continues to spread in brazil causing unprecedented challenges to the country's health system. herein, we described the epidemiological and clinical manifestations of the first 557 successive covid-19 patients in pernambuco state, northeast brazil. our study provided important information about the demographics, clinics and epidemiology of covid-19 in the tropical world and will assist physicians and health officials to face the current pandemics and be better numbers between parentheses indicate percentage of patients in each age group. prepared to counteract future incursions of highly transmissible respiratory pathogens in the human population. the authors declare no conflict of interest. clinical features of patients infected with 2019 novel coronavirus in wuhan, china a novel coronavirus from patients with pneumonia in china a pneumonia outbreak associated with a new coronavirus of probable bat origin covid-19) -situation report -51 brasil confirma primeiro caso de infecção pelo novo coronavírus. 2020. htt ps://www.paho.org/bra/index.php?option=com_content&view=article&id=6 113:brasil-confirma-primeiro-caso-de-infeccao-pelo-novo-coronavirus&itemi d=812 covid-19 in latin america: the implications of the first confirmed case in brazil what are the factors influencing the covid-19 outbreak in latin america boletim epidemiológico covid-19. recife. pernambuco: state health department covid-19 in brazil: "so what? clinicalmanagement-of-severe-acute-respiratory-infection-when-novel-coronavirus-(ncov)-infection-is-suspected detection of 2019 novel coronavirus (2019-ncov) by real-time rt-pcr effect of income on the cumulative incidence of covid-19: an ecological study importation and early local transmission of covid-19 in brazil clinical characteristics of coronavirus disease 2019 in china estimates of the severity of coronavirus disease 2019: a model-based analysis coronavirus disease 2019 (covid-19): epidemiology update 2020 impact of sex and gender on covid-19 outcomes in europe gender differences in patients with covid-19: focus on severity and mortality 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 clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study clinical characteristics of 140 patients infected with sars-cov-2 in wuhan, china. allergy clinical features and treatment of covid-19 patients in northeast chongqing viral dynamics in mild and severe cases of covid-19 characterization and clinical course of 1000 patients with coronavirus disease 2019 in new york: retrospective case series covid-19 and comorbidities: a systematic review and meta-analysis supplementary data to this article can be found online at https://doi. org/10.1016/j.tmaid.2020.101884. key: cord-287488-h102xn29 authors: araujo, danielle bastos; machado, rafael rahal guaragna; amgarten, deyvid emanuel; malta, fernanda de mello; de araujo, gabriel guarany; monteiro, cairo oliveira; candido, erika donizetti; soares, camila pereira; de menezes, fernando gatti; pires, ana carolina cornachioni; santana, rúbia anita ferraz; viana, amanda de oliveira; dorlass, erick; thomazelli, luciano; ferreira, luis carlos de sousa; botosso, viviane fongaro; carvalho, cristiane rodrigues guzzo; oliveira, danielle bruna leal; pinho, joão renato rebello; durigon, edison luiz title: sars-cov-2 isolation from the first reported patients in brazil and establishment of a coordinated task network date: 2020-10-23 journal: mem inst oswaldo cruz doi: 10.1590/0074-02760200342 sha: doc_id: 287488 cord_uid: h102xn29 background: severe acute respiratory syndrome coronavirus 2 (sars-cov-2) was confirmed in brazil in february 2020, the first cases were followed by an increase in the number of cases throughout the country, resulting in an important public health crisis that requires fast and coordinated responses. objectives: the objective of this work is to describe the isolation and propagation properties of sars-cov-2 isolates from the first confirmed cases of coronavirus disease 2019 (covid-19) in brazil. methods: after diagnosis in patients that returned from italy to the são paulo city in late february by rt-pcr, sars-cov-2 isolates were obtained in cell cultures and characterised by full genome sequencing, electron microscopy and in vitro replication properties. findings: the virus isolate was recovered from nasopharyngeal specimen, propagated in vero cells (e6, ccl-81 and hslam), with clear cytopathic effects, and characterised by full genome sequencing, electron microscopy and in vitro replication properties. virus stocks viable (titre 2.11 × 10(6) tcid50/ml, titre 1.5 × 10(6) pfus/ml) and inactivated from isolate sars.cov2/sp02.2020.hiae.br were prepared and set available to the public health authorities and the scientific community in brazil and abroad. main conclusion: we believe that the protocols for virus growth and studies here described and the distribution initiative may constitute a viable model for other developing countries, not only to help a rapid effective pandemic response, but also to facilitate and support basic scientific research. mild upper respiratory tract disease with low mortality rates. (1) however, in 2003 and 2012, respectively, the emergence of highly pathogenic severe acute respiratory syndrome (sars-cov) (2) and middle east respiratory syndrome (mers-cov) (3) revealed that this virus group may also cause severe respiratory illness in humans. in december 2019, in wuhan, china, a novel coronavirus, member of the β coronavirus family, has been identified as the source of a pneumonia outbreak (4) and this novel virus was named as severe acute respiratory syndrome coronavirus 2 (sars-cov-2), by the international committee on taxonomy of viruses (ictv). (5) in brazil, the four endemic covs circulate annually (6) (7) (8) (9) (10) (11) and the first case of coronavirus disease 2019 (covid19) was reported on february 26, 2020 (https://covid.saude. gov.br) when sars-cov-2 was detected in a 61-year-old male traveller from lombardia region, italy, that returned to the são paulo city, brazil. until the first reported case in brazil, also the first in south american region, (12) there were 81,109 confirmed covid-19 cases in 38 countries. after these first reported patient, cases in brazil started to rise reaching 3,846,153 infected persons and 120,462 deaths on august 29 (https://covid.saude.gov.br). isolation and propagation of new viruses in vitro represents an essential step and may generate important primary tools in early outbreak characterisation. in that way, isolation of the virus presently disseminating in brazil will provide important information regarding diversity and molecular evolution of the pathogen, but also supply reference material in the struggle to control the rampant spreading of the pandemic sars-cov-2 in the country. indeed, the availability of infective particles as well as inactivated genetic material as reference reagents are extremely necessary for the preparation of positive controls in molecular diagnosis, development of vaccine formulations, detection of neutralising antibodies, screening of antiviral compounds and for different basic research projects both for public health reference laboratories and the research community. in this study, we describe the isolation of sars-cov-2 from the first two patients diagnosed with the novel coronavirus disease in brazil. we describe its genomic sequence (sars-cov-2/sp02/human/2020/bra) and in vitro replication characteristics. virus stocks (infectious particles and lysates) were set available and distributed to the research community. ethics declarations -all methods were performed in accordance with relevant guidelines and regulations. this work was approved by the ethics committee on research with humans from the institute of biomedical sciences, university of são paulo, brazil (permission number 74683917.1.0000.5467). all specimens were handled under the laboratory biosafety guidance required for the novel coronavirus (2019-ncov) by the world health organization (who) (13) at bls3 facilities at the institute of biomedical sciences, university of são paulo. clinical specimen collection -nasopharyngeal (np) swab samples were collected from symptomatic patients who had acquired covid-19 during travels to northwest of italy (lombardia region) and returned to the são paulo city in late february. these patients were treated in the same hospital and were the two first confirmed cases of covid-19 in the são paulo city. the specimens were collected on day 2-4 post-symptom onset, placed in 1-2 ml of saline medium and used for molecular diagnosis and virus isolation. nucleic acid extraction and real-time rt-qpcr for virus detection -in order to perform the identification of sars-cov-2, the extraction of total nucleic acid (rna and dna) from the collected samples (200 µl of initial material) were carried out using the semi-automated nuclisens ® easymag ® platform (biomérieux, lyon, france), following the manufacturer's' instructions. all specimens were handled under the laboratory biosafety guidance required for the novel coronavirus (2019-ncov) by who (13) at bls3 facilities at the institute of biomedical sciences, university of são paulo. the de-tection of viral rna was carried out using the agpath-id one-step rt-pcr kit (applied biosystems inc., waltham, usa) on an abi 7500 sds real-time pcr machine (applied biosystems, weiterstadt, germany), using a published protocol and sequence of primers and probe for e gene. (14) rna copies/ml was quantified by real-time rt-qpcr using a specific in vitro-transcribed rna quantification standard, kindly granted by christian drosten, charité -universitätsmedizin berlin, germany, as described previously. (2) virus isolation -we used vero e6 cells for isolation and initial passages. we cultured vero e6 in dulbecco minimal essential medium (dmem) supplemented with 10% of heat-inactivated foetal bovine serum (fbs) (vitrocell embriolife, campinas, brazil). we used np swab specimen for virus isolation. for isolation and first passage, we sow cells in a 25 cm 2 cell culture flask in a concentration of 5 × 10 5 cells/ml. after 24 h, we removed the culture medium, washed three times with fbs free-dmem and inoculated aliquots (500 μl) of the clinical specimens into the flask. after 1 h of incubation (adsorption), we completed the volume for 5 ml with dmem supplemented with 2.5% fbs and 1% of penicillin-streptomycin. we grew the inoculated cultures in a humidified 37°c incubator in an atmosphere of 5% co 2 and observed for cytopathic effects (cpe) daily up to 72 h. supernatant was collected daily, and virus replication was confirmed through cpe, gene detection and electron microscopy. virus titration -median tissue culture infectious dose (tcid 50 /ml) -vero e6 and ccl-81 cells were seeded into 96-well plate (5 × 10 4 cells/ml), 24 h before the experiment. virus was 10-fold serially diluted in medium (10 -1 to 10 -12 ). medium was removed from plates, virus dilutions applied in sextuplicate and incubated at 37°c. visualisations were performed daily in an inverted light microscope (axiovert 100, carl zeiss oberkochen) to observe the cpe. after 72 h, the last reading was performed, and the monolayers were fixed and stained with naphthol blue black (sigma-aldrich co., deisenhofen, germany) dissolved in sodium acetate-acid acetic. the viral titre was expressed in tcid 50 /ml and calculated using the spearman & kärber algorithm, as described by hierholzer & killington. (15) plaque forming units (pfu/ml) -virus titration was carried out in 24 wells plates seeded with vero e6 and ccl-81 cells at a concentration of 1 × 10 5 cells/well. after 24 h and a cell confluence of 80-90%, dilutions 10 -1 to 10 -10 in dmem 2.5% fbs of the virus was transferred in duplicate (100 µl/well) to the seeded plates. after 1 h adsorption at 37 o c 5% co 2 , the wells were completed with an overlay of carboxymethyl cellulose (cmc) with dmem, 2% fbs and 1% of penicillin-streptomycin, and plates incubated at 37 o c in 5% co 2 and stained with naphtol blue black dissolved in sodium acetate-acid acetic. plates were observed and stained from 48 to 96 h post-inoculation (h.p.i.). both virus titration (tcid 50 / ml and pfu/ml) were made after the third passage of the isolated virus (t2). samples were adsorbed to glow-discharged carbon filmcoated copper grids (400 mesh, cf400-cu, electron microscopy sciences). the grids were washed with ultrapure water treated with depc and negatively stained with uranyl acetate 2% (w/v) with blotting on filter paper after each step. a fei tecnai g20 200 kv transmission electron microscope (department of cell and developmental biology, institute of biomedical sciences, university of são paulo) was used for image acquisition. virus growth kinetics in different cell lines -three vero cell lines (e6, ccl-81 and hslam) plus a human epithelial type 2 (hep-2) cells, at concentration of 5 × 10 4 cells/ml, were tested for the propagation of the sars-cov-2 by inoculation at a multiplicity of infection (moi) of 0.02. the culture medium consisted of dmem supplemented with 2.5% of fbs. aliquots of cell-associated and supernatants compartments were collected every 12 h up to 96 h.p.i. for virus quantification via tcid 50 / ml and rna copy number quantification by reverse transcription-quantitative polymerase chain reaction (rt-qpcr). the assay was conducted in triplicate, reproduced in two independent experiments and expressed by standard error of the mean (sem). graphics and sem were done using graphpad prism software version 8.1 (graphpad software, san diego, usa). next generation sequencing of viral full-length genome -we extracted total nucleic acid from the np and oropharyngeal (op) swab samples and cell supernatants isolates with the qiaamp viral rna mini kit (qiagen, hilden, germany). the purification and concentration steps were carried out with rna clean & concentrator kit (zymo research, irvine, usa) with dnase i treatment during the concentration process. depletion of human ribosomal rna was performed with the concentrated rna product using the qiaseq fast select rna removal kit (qiagen). finally, the rna samples were submitted to random amplification following the methodology described in greninger et al. (16) with few modifications. the preparation of sequencing libraries for the illumina platform was carried out with the nextera xt kit (illumina, san diego, usa) and multiplex testing, using the random two-step pcr amplification product as input, followed the kit's standard instructions. the libraries were quantified after fluorescence measuring with the qubit instrument (thermo fisher scientific, waltham, usa) and loaded on the nextseq 550 equipment (illumina) for sequencing with mid 300 pairedend reads (illumina). sequencing analysis -the sequencing data was analysed by a flow of bioinformatics analysis (pipeline) developed at albert einstein hospital. in summary, raw sequencing data was subjected to sequence quality controls, removal of human contaminants by aligning against the hg19 reference genome, taxonomic identification of other pathogens and genome recovery through manual curing. quality control was performed using cutadapt (17) to filter sequences by length (< 50 bp), average quality (q p < 20) and trim options to remove low quality ends (9 bp to 5' end and 5 bp to 3' end). passed qc reads were mapped to hg19 human reference genome using bwa (18) mem with default parameters. not mapped reads were submitted to assembly using spades 1.13. (19) contigs were inspected and manually curated using geneious 2020.1 to generate a final assembly. complete genome was compared to sars-cov-2 reference and close isolates by multiple sequence alignment. final genome was deposited in genbank (https:// www.ncbi.nlm.nih.gov/genbank/). the preparation of vis and vls stocks was performed as described above for virus isolation. clinical specimen collection -patient 1 (hiae01), a 61-years-old male patient, and patient 2 (hiae02), a 32-years-old male patient, had returned from northwest of italy (lombardy region) and presented respiratory symptoms including cough, sore throat, runny nose, fever, myalgia and headache. patient 1 was initially diagnosed with a community-acquired pneumonia and received antimicrobial therapy. both were confirmed for covid-19 by hospital israelita albert einstein (hiae), in the são paulo city on february 26 (hiae01) and 28 (hiae02), 2020. a summary of clinical characteristics of the patients is described in table. lombardy is considered the centre of the covid-19 outbreak in italy (20) and has a high influence of the first wave of sars-cov-2 introduced in brazil. (21) virus isolation -before isolation in cell cultures, we tested the samples using a one-step multiplex rt-qpcr for the detection of 18 additional different respiratory viruses (22) and tested for bacterial contamination using fluid thioglycolate medium (becton dickinson, franklin lakes, usa). no other pathogens were detected. the positive np were inoculated on vero e6 cells. the initial sample collected from hiae01 was freezed and thawed before inoculation and no virus propagation was obtained. a second sample, from the same patient, was obtained "fresh" (conserved at 4ºc for no longer than 12 h) and we could successfully isolate sars-cov-2. sample from hiae02 was inoculated "fresh" from the first moment. the failure to isolate the virus from the first sample collected from hiae01 may be attributed to a lower virus load and to the freeze-thaw cycle before cell culture inoculation. the schematic timeline of procedures is presented at fig. 1 . three days post infection, the isolation of sars-cov-2 from hiae02 was confirmed by rt-qpcr, electron microscopy and whole genome sequencing (fig. 1) . the cycle threshold (ct) value and genome copy numbers (rna copies/ml) of the pre-inoculated sample was ct 17.49 and 8.46 × 10 6 (fig. 2a) . rna quantification of passages 2 and 3 after 72 h.p.i. gave values of 10.12 -1.19 × 10 9 copies/ml and 9.22 -2.18 × 10 9 copies/ml, respectively. since virus isolation from hiae02 (sars.cov2/sp02.2020.hiae.br) was faster, all the subsequent studies were carried out with this isolate after passage 3. virus isolation (passage 0) from hiae01 (sars.cov2/sp01.2020.hiae.br) was confirmed by rt-qpcr (ct 15.02 -4.4 × 10 7 copies/ml) and whole genome sequencing, being stored at -80ºc. negative staining transmission electron microscopy of the sars.cov2/sp02.2020.hiae.br, here after referred as sp02/bra, permitted the observation of coronavirus-specific morphological structure, being possible to visualise the protein components of the viral envelope. the virus particle size ranged from 80 to 100 nm (fig. 2b ). the cpes were characteristic of sars-cov-2: cell rounding, detachment of the cell monolayer and formation of loose cells on the surface, for both vero e6 and ccl-81 cells and similar to previously observed effects. (23) (24) (25) (26) nonetheless, the cpes were more evident in ccl-81 cells. the virus isolate was titrated after two blind passages following isolation (t2) and the cpes were more clearly observed in ccl-81 cells for tcid 50 /ml (2.11 × 10 6 ) and pfus (1.5 × 10 6 ). for pfus titration, effects were not clear for vero e6 cells, and for vero ccl81, only a few small plaques were visible at 72 h.p.i., being much larger and more visible at 96 h.p.i. (supplementary data, fig. 1 ). hartcourt et al. (23) described effects more visible for vero e6 cells when compared to ccl-81. other successful sars-cov-2 isolation reports were based on vero e6, vero ccl-81 and vero hslam (23) (24) (25) (26) (27) showing that the three cell lines are permissive for sars-cov-2. virus growth kinetics in different cell lines -we examined sars-cov-2 growth kinetics in three vero cell lines (e6, ccl-81 and hslam) and compared with hep-2 cells. all cells were inoculated with the sars-cov-2 isolate (sp02/bra) and cultured under similar conditions. virus titre quantification analysis of cell-associated and supernatants compartments indicated that similar levels of infectious sars-cov-2 were produced in all three vero cell lines of vero, but not in hep-2 cells, that proved to be not permissive to virus replication. the peak of viral titre was detected 48 h.p.i. (10 7 tcid 50 /ml) after an initial eclipse phase. cpes was not observed until 48 h.p.i. and reached a peak at 72 h.p.i. (supplementary data, fig. 2 ). quantification of ribonucleic acid copy number (rna cn ) indicated that virus was released into the supernatant with similar kinetics for all three tested vero cell lines, with virus yielding slightly higher values on 72 h.p.i. (fig. 3b) . rnacp:tcid 50 ratios did not differ significantly (p > 0.05) among the tested vero cell lines (fig. 3c ). in addition, these cell lines appeared to release few noninfectious particles at early time points of the infection. the rnacp:tcid 50 ratios appeared to increase discreetly over time, suggesting an increase in the release of noninfectious virus at later time points or an increase in virus particle degradation over time (perhaps as a consequence of cell culture proteases). virus rna was not detected in the cell-associated fraction and cell cultures supernatants of hep-2 cells (fig. 3a , b). any clear-characteristic cpe of sars-cov-2 was observed in hep-2 cells (supplementary data, fig. 2) . similarly to other studies with sars-cov (28, 29) and sars-cov-2, (23, 26) our findings demonstrated that the three tested vero cell lines release infectious virus particles and viral rna copies at the same kinetics and efficient egress. whole genome sequencing -whole genome sequence of the sars-cov-2 wuhan-hu-1 (nc_045512) and inmi 1/ita (mt066156) were compared with sp02/ bra directly isolated from patient's sample (mt126808) and after cultivation in vero cells (mt350282) using mafft multiple aligner tool (algorithm = auto and pam = 1). alignment shows only two mutations at the cultivated strain (> 99.993% similarity). mutations occurred at the nsp2 and spike proteins (fig. 4) . distribution network -until march 20, 2020, the sending of the material comprised 31 different research groups, in public and particular university/hospitals, at 10 different states in brazil (fig. 5) . the inactivated virus (vls) was distributed according of request from the laboratories to testing clinical samples by rt-qpcr, using the vls as positive controls, which was important, considering the difficulties -availability and price -to import synthetic rna in brazil. the criteria for distributing live virus (vis) was based in the capacity of bsl3 facilities from the host institutions, experience of the principal investigator and the analysis of priority for development of vaccine, drug discovery and virus neutralisation diagnosis. this initiative is crucial to improve the study of sars-cov-2 and the development of methods and strategies for virus treatment and prevention. sarscov-2 isolates were set available to the scientific community by different groups in other countries. (23, 27) the first delivery to the research community at the são paulo state was set on march 13. the virus distribution by the brazilian mail company was first set on march 18, 2020 and, in less than 13 h, the biological material was delivered to rio de janeiro (222.26 miles away from the são paulo city), the state of minas gerais (304.28 miles) and the state of rio grande do sul (815.94 km). virus samples were sent following technical and biosafety requirements, in accordance with anvisa recommendations. in conclusion, in this work, we describe the successful isolation of sars-cov-2 from the first diagnosed patients in brazil. the virus was propagated in vero cell lines and replication features, cpe and growth kinetics were described. the experimental protocols described herein can be used for future attempts to isolate sars-cov-2 in different places in the world. the produced virus stocks were distributed to different research groups and hospitals in the country and are being used as a reference in diagnostic tests and for research, aiming the screening of antivirus drugs, testing the efficacy of vaccine formulations under experimental conditions. the vls are been used as controls for molecular diagnosis and studies, eliminating the need of imported material in the first weeks of the pandemic in brazil. the covid-19 pandemic is unprecedent and the collaborative work is crucial to the efforts to understand and control the virus spread in the country. data availability -the complete genome sequences of sars-cov-2/sp02/human/2020/bra from de clinical sample and sars-cov-2/human/bra/ sp02cc/2020 from cell culture isolation have been deposited in the genbank (accession mt126808 and mt350282, respectively). the version described in this paper is the first version. epidemiology, genetic recombination, and pathogenesis of coronaviruses identification of a novel coronavirus in patients with severe acute respiratory syndrome isolation of a novel coronavirus from a man with pneumonia in saudi arabia a novel coronavirus from patients with pneumonia in china the species severe acute respiratory syndromerelated coronavirus: classifying 2019-ncov and naming it sars-cov-2 human coronavirus and severe acute respiratory infection in southern brazil human coronavirus occurrence in different populations of são paulo: a comprehensive nine-year study using a pancoronavirus rt-pcr assay human coronavirus nl-63 infection in a brazilian patient suspected of h1n1 2009 influenza infection: description of a fatal case public health awareness of emerging zoonotic viruses of bats: a european perspective coronavirus hku1 in children, brazil typical epidemiology of respiratory virus infections in a brazilian slum covid-19 in latin america: the implications of the first confirmed case in brazil laboratory biosafety guidance related to the novel coronavirus (2019-ncov) detection of 2019 novel coronavirus (2019-ncov) by realtime rt-pcr virus isolation and quantitation rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis cutadapt removes adapter sequences from highthroughput sequencing reads fast and accurate short read alignment with burrows-wheeler transform spades: a new genome assembly algorithm and its applications to single-cell sequencing spread and dynamics of the covid-19 epidemic in italy: effects of emergency containment measures routes for covid-19 importation in brazil comparison of fast-track diagnostics respiratory pathogens multiplex real-time rt-pcr assay with in-house singleplex assays for comprehensive detection of human respiratory viruses severe acute respiratory syndrome coronavirus 2 from patient with 2019 novel coronavirus disease, united states virus isolation from the first patient with sars-cov-2 in korea serological and molecular findings during sars-cov-2 infection: the first case study in finland 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 isolation and rapid sharing of 2019 novel coronavirus (sars-cov-2) from the first patient diagnosed with covid-19 in australia sars-associated coronavirus replication in cell lines discovery of novel human and animal cells infected by the severe acute respiratory syndrome coronavirus by replicationspecific multiplex reverse transcription-pcr to roberto cabado, for technical assistance at the electron microscopy facilities at department of cell and developmental biology, institute of biomedical sciences, university of são paulo, to priscila perine, for viral purification and concentration, to the lvcm covid-19 working group members (bruna larotonda telezynski, camila araujo valério, fabyano bruno leal, ralyria mello and vanessa nascimento chalup), and to the brazilian mail company and the mctic of brazil, for the logistic support in virus distribution. key: cord-305936-tdswzj7r authors: freitas, andré ricardo ribas; donalisio, maria rita title: excess of mortality in adults and elderly and circulation of subtypes of influenza virus in southern brazil date: 2018-01-08 journal: front immunol doi: 10.3389/fimmu.2017.01903 sha: doc_id: 305936 cord_uid: tdswzj7r purpose: in the elderly population, the influenza infection and its clinical complications are important causes of hospitalization and death, particularly, in longer-lived age. the objective of this study is to analyze the impact of influenza virus circulation on mortality in the elderly and adults, in years with different predominant virus strains. methods: we performed a time trend study to evaluated excess of mortality for pneumonia and influenza, respiratory disease, and all-causes in southern region of brazil, from 2002 to 2015. after considering other models, we opted for serfling regression. excess of death rates per 100,000 inhabitants were analyzed in specific age groups (24–59, 60–69, 70–79, ≥80 years) and by year of occurrence. mortality information were taken from brazilian mortality information system and etiological data were accessed in sentinel virological surveillance database, getting the weekly positivity of the immunofluorescence tests for influenza a (h1n1, h3n2), and b. results: in southern brazil, there is an evident seasonal pattern of all death outcomes among different age groups in the dry and cold season (april–september). the highest excess mortality rates occurs among older, particularly in years of circulation of influenza ah3n2, especially among people ≥80 years, in 2003 and 2007—years of great severity of influenza activity. after 2009, with the introduction of the pandemic influenza ah1n1, we observed a lower impact on the mortality of the elderly compared to <60 years. discussion: a cross reactivity antibody response from past exposure probably provided protection against disease in the elderly. despite not controlling for comorbidities, climate, and vaccination, for the >70 years, ratio of respiratory diseases excess mortality rates between ah1n1 (2009) and severe year of h3n2 (2007) shows protection in the pandemic year and great vulnerability during ah3n2 virus predominance. conclusion: the reduced immune response to infection, and to vaccination, and presence of comorbidities recommend a special attention to this age group in brazil. besides medical assistance, the timeliness of vaccine campaigns, its composition, and etiological surveillance of respiratory diseases are some of the preventive and public health measures. introduction human influenza viruses can cause diseases through many direct and indirect pathological effects. consequences are destruction of infected cells, release of cytokines leading to fever, malaise, damage to respiratory epithelium and pulmonary parenchyma, and pneumonia. it includes secondary bacterial infections because of tissue damage and exacerbation of preexisting comorbidities such as cardiovascular and renal diseases, diabetes, or chronic lung disease (1) (2) (3) . the rates of hospitalization and mortality associated with influenza are higher among patients with chronic diseases, children under 1 year and after 65 years of age (4, 5) . with the aging population in recent decades, the raw number of hospitalizations and deaths related to pneumonia and influenza tends to increase (4) , this phenomenon has been observed also in brazil (6, 7) . however, the impact and severity of influenza virus circulation depend in part, on the strain that predominates in the season each year. due to the lack of laboratory confirmation, influenza-associated morbidity and mortality are often classified as pneumonia, other respiratory diseases, or other causes. given the difficulty of directly measuring influenza morbidity and mortality, time series models are used to elucidate disease patterns in various age groups. trends are usually determined by means of statistical inference, based on seasonal coincidence of the occurrence of certain diseases or death and laboratory confirmation of the viral circulation (4, 8) . different approaches, with and without the quantification of the proportion of viral isolates, can produce average estimates of excess deaths associated with the circulation of certain viral variants (9) (10) (11) . viral surveillance data, hospitalization, or death indicators are particularly useful for the study of influenza in the tropics, as seasonality may be less evident (11) (12) (13) . serfling regression has been used to analyze excess of mortality related with respiratory virus circulation (7, (14) (15) (16) . despite some limitations (17) , the inclusion of sinusoidal terms in weekly regression may reduce spurious correlation between influenza occurrence and death (18, 19) . it is particularly useful when no other covariables are available, and with small samples of viral sentinel surveillance data (18) . poisson regression and the generalized linear model (glm) can produce more specific estimates and support adjustments for variables (temperature, humidity, comorbidities, other circulations of viruses), although they require a more robust and consistent virological surveillance and cannot be used for pandemics (4) . in brazil, surveillance for influenza syndromes was implemented in 2000, monitoring the occurrence of respiratory viruses (influenza a and b, parainfluenza 1, 2, and 3, respiratory syncytial virus, adenovirus). the brazilian ministry of health provides vaccination coverage annually since 1999 for seniors and some risk groups, with vaccine coverage of the elderly population at around 80% in southern brazil, the region with the highest coverage of the country. despite the adequate coverage, protective titers after vaccination (hi ≥ 0) are consistently lower with poorer cell mediate and antibody responses in the elderly comparing to adults (20) . considering the vulnerability of the elderly to influenza virus infection, and the lack of studies on its repercussion in brazil, the objective of this study was to analyze the impact of different strains of influenza a virus circulation. we analyzed particularly the most predominant variants (ah1n1 and ah3n2) on excess of mortality in the adults and elderly of different age groups in a region with marked seasonality of respiratory diseases in brazil. this is a time trend study to evaluated excess of mortality from 2002 to 2015 in southern region of brazil (states of paraná, santa catarina e rio grande do sul), total area is 576,774,31 km 2 , population is 27,386,891 inhabitants with subtropical climate (köppen-geiger classification cfa). we choose these states for analysis because of the consistent seasonal pattern of influenza, as well as the availability and quality of etiological data from the virological surveillance system in that region. for the mortality rates of specific age groups (24-59, 60-69, 70-79, and ≥80 years) and death causes, we took data from brazilian mortality information system. causes are classified according to international causes of death icd-10 revision, pneumonia, and influenza (icd j 10 to j18.9), respiratory diseases (icd j00 to j99), and all-cause (excluding external causes of mortality). we obtained population of each year and age group from instituto brasileiro de geografia e estatística-ibge from the census-2010, and population estimates for the following years. etiologic information of flu-like syndrome was accessed in database of the national sentinel virological surveillance system. it has data from 128 sentinel units distributed in all regions of the country-north (21 units), northeast (26 units), southeast (34 units), south (38 units), and central west (9 units). surveillance is performed through the systematic collection of weekly samples of nasopharyngeal secretions from patients who present flu-like syndrome. reference laboratories process samples by using indirect immunofluorescence (iif), with tests for influenza a and b, parainfluenza 1, 2, and 3, respiratory syncytial virus, and adenovirus. a portion of the samples is submitted to polymerase chain reaction tests to identify the virus genotype. we calculated the laboratory positivity indicator using weekly positive results of iif divided by the total of weekly valid tests, i.e., excluding the results within inadequate samples (not enough biological material, improper storage, incorrect material in the sample) or inconclusive results (no valid results). influenza vaccination coverage (%) of southern region from 2002 to 2015 was obtained from brazilian national program of immunization data base (datasus). the criteria used to define the period of increase of influenza activity was when the positivity of the samples tested exceeded twice the annual mean of the weekly positivity of samples processed by surveillance, during two consecutive weeks. in the year 2009, we consider the period officially recognized by the brazilian ministry of health as epidemic by the influenza ah1n1pmd2009 strain, due to irregularity of the sample collection by the sentinel surveillance system at the end of epidemic. we calculated the weekly mortality rates by age group using the number of deaths per group of causes divided by the estimated population in the middle of the year multiplied by 100,000. we constructed a serfling cyclical regression model (14) for weekly data applied to each age group and causes of death (pneumonia and influenza, respiratory diseases, and all causes), as seen in others studies (7, 15) , to estimate baseline of predicted deaths in the absence of influenza epidemics. to fit regression, we used period of 13 years (from 2002 to 2015), excluding the weeks of epidemics periods. a cyclical linear regression was adjusted with the equation: where y is the mortality rate, β is the coefficients of regression, t is time in weeks, and t 2 and t 3 are variables for adjusting the secular trend of the disease. we used of sine and cosine for adjust of annual and semiannual periodic components. after adjusting a linear regression and define the expected mortality rate, we delimited 95% upper confidence limit of the baseline as the reference threshold in the absence of influenza epidemics. we calculated the excess of deaths as the observed mortality minus the expected mortality in the periods when mortality was above 95% of the confidence interval during epidemics periods. we also present ratios of excess mortality rates among years of predominant circulation of influenza strains ah3n2 (mean and years of severity), ah1n1 pre-pandemic, and ah1n1 postpandemic for each age group. for data compilation, we used microsoft office excel 2007, and for statistical analysis, spss for windows, version 24.0. results table 1 shows the proportion of positivity of the iif nasopharyngeal samples and the annual prevalence of strains of influenza in the period. before 2009, the year of entry of the pandemic strain ah1n1pmd 2009, there was a predominance of influenza ah3n2 in the years 2003 to 2007. after 2009, there is alternation of strains in the southern brazil. annual elderly vaccination coverage in southern region is high and homogeneous, around 80%, and even higher in the recent years. there is an evident seasonal pattern of deaths from pneumonia and influenza, respiratory diseases, and all-causes among the elderly in different age groups in the dry, cold months (april-september) in southern region (figure 1) . we note a progressive increase in the rates of excess deaths (of all outcomes) with increasing age, especially among those older than 70 years. in the pre-pandemic years with dominance of the ah1n1 strain, the excess of mortality rates associated with influenza were relatively low, compared to years of prevalence of ah3n2 strain ( table 2) . among those over 80 years, the ratio of excess mortality rates between 2009 and the years with dominium of h3 strains was less than one. this ratio suggests that this age group was spared in the 2009 pandemic. however, in years of predominance of strain h3, excess of mortality rate of all causes in this group were 449.6 per 100,000 (corresponding to 1,598 obits), 5, and 8.2 times greater than the same rate in years of circulation of h1n1 in pre-and post-pandemic period, respectively. among adults (24-59 years), we observe a large excess of deaths rates during the 2009 pandemic (953 obits), which correspond to 7.1 excess deaths from all causes, and 99 excess mortality from respiratory diseases associated with viral infection in every 100,000 individuals of the age group. the ratio between excess mortality rates due to pneumonia/influenza in the pandemic year (2009) and the mean rate of the period was 12 times higher among the youngest ( table 2) . rates of excess mortality by pneumonia and influenza and respiratory diseases are lower than all causes in all age groups, but particularly high in older than 80 years ( table 2) . the results highlight the great vulnerability of elderly to influenza ah3n2, especially among older than 70 years in severe years of influenza activity, like 2003 and 2007. the study also shows the lower impact of influenza ah1n1pdm 2009 in this age group compared to younger. risk of dying among the elderly in years of circulating ah3n2 influenza has been reported in several parts of the world (9, 10, 21, 22) ; however, in brazil, there are no recent estimates available. few studies analyze the circulation and impact of influenza in tropical and subtropical regions (6, 7, (9) (10) (11) . influenza b virus is also associated with severe disease (23); however, this variant did not circulate with intensity during the study years in brazil. although the elderly are the most vulnerable group to viral respiratory infections, we found relative small excess of deaths in years of circulating ah1n1 pre pandemic (2002 and 2008) . study comparing excess deaths from respiratory diseases in the elderly in latin america shows stable rates (mean of 89.4 per 100,000 inhabitants) in southern brazil between 1998 and 2008 (prepandemic flu a-h1n1), although higher in brazil than in other countries (24) . in the usa and in european countries, influenza seasons dominated by subtype ah3n2 are typically associated with mortality two to three times higher than in seasons with predominance of ah1n1 (prior to pandemic strain 2009) and of influenza b viruses (9, 10, 19, 25) . when all causes of death are studied, the overall mortality associated with influenza among elderly exceeds that observed in younger age group. it should be considered that all causes mortality is a non-specific measure and a distant outcome of influenza infection. however, it is difficult to determine which group of causes of death could better characterize the influenza burden in mortality. by choosing only the respiratory causes, we may underestimate clinical complications of pulmonary viral infection (e.g., cardiovascular). therefore, in this study, we analyzed all causes, respiratory, and pneumonia and influenza deaths. the unfavorable evolution of infection in the elderly is possibly due to the prevalence of comorbidities, deficiencies in defense mechanisms, and poor antibody response to vaccination, as cellmediated and humoral responses limit severity of disease (26) . patients with chronic diseases are more susceptible to infection due to decline of the immune function through inflammatory mechanisms, hindering the mucosal barrier, and the adaptive and innate immunological defense mechanisms (27) . the immune response to infection in the elderly tend to be delayed and weak, with prolonged inflammatory responses, which involves different types of host reaction, mainly to clearance virus. the exacerbations of these mechanisms may induce immunemediated pathology causing tissue damage (28) . cytokine high serum levels of il-6, tnf-a, ifn-g and sil-2r, chemokines ip-10, mcp-1, and monokine induced by ifn-g (mig), are associated with severe clinical cases and lung damage (29) . immunological abnormalities in people with diabetes, chronic respiratory diseases, cardiopathy, or other chronic diseases have increased risk of severe infection and bad prognosis (19) . for example, there is the consistent association of influenza infection with cardiovascular mortality, particularly acute myocardial infarction (30) . in part, it is attributed to altering endothelial function due to an acute inflammatory and procoagulant stimulus during viral infection (31, 32) . clinical complications of diabetes triggered by influenza infection cause impairment of leukocyte function and increase post-infection colonization rates resulting in poor prognosis in the elderly (33, 34) . in young people and adults, in 2009, the emerging influenza ah1n1 strain had a notable impact on the mortality of people up to 59 years in various parts of the world, including brazil (7, 25, 35, 36) . excess mortality of individuals aged 24-59 years in the state of são paulo, brazil was identified during the pandemic ah1n1 virus (7) . pregnant women adults with metabolic conditions, including obesity, chronic respiratory disease, and other chronic diseases were significantly associated with severe acute respiratory syndrome and the lethality in brazil (37) . our study showed a 41.5-fold higher rate of mortality from pneumonia and influenza in adults (24-59 years) in the pandemic year ah1n1 than the average of years with predominance of ah3n2 circulation in southern region. in addition to the clinical severity and the large portion of the affected population, pandemics affect age groups in different ways (38) . while only 10% of deaths from seasonal influenza occur among those under 65 years of age, in the pandemics of 1918, 1957-1958, and 1968 , this proportion was 95, 40, and 50%, respectively (39) . therefore, pandemics tend to affect a larger proportion of young people than seasonal influenza. in this study, higher rates of death due to pneumonia, influenza, respiratory, and all causes were observed among those aged 24-59 years in 2009. one explanation for the higher mortality observed among the youngest is that they would be more prone to the situation known as "cytokine storm, " i.e., a dysfunctional overproduction of cytokines that would lead to diffuse damage to the respiratory tract with severe and potentially lethal systemic repercussions (40) . viral replication and production of inflammatory mediators seem to be involved in the pathogenesis of infection with influenza a h1n1pmd2009, hindering the clearance of virus in lung tissue and leading to pathologic lesions (41) . another explanation for the lower mortality in the elderly is that they were exposed previously to antigens of the pandemic virus. hancock et al. (42) suggested a cross-reactive antibody response to 2009 pandemic ah1n1. similarities between ah1n1 antigen from 2009 and 1918 were detected. this last virus strain has not circulated since 1958 (39) , when the ah1n1 strain was displaced by ah2n2 (asian flu). at that time, ah1n1viral circulation occurred mainly in children, the current elderly of 2009. the emergence of the ah3n2 strain in the pandemic year 1968 (hong kong flu) affected several age groups. this new strain resulted from a large genetic mutation (shift) recombining virus material of the circulating ah2n2 with the avian h3, of asian origin, resulting in the new variant ah3n2 (38) . in 2002-2003, under selective pressure an antigenic small mutation (drift), resulted in a/fujian/411/02(h3n2) a strains emerged after a "jump" in genes evolution of hemagglutinin and neuraminidase proteins of virus surface (43, 44) . the circulation of the fujian strain had a great impact on the mortality from pneumonia in several parts of the world in 2003-2004 and 2004-2005 (22) and in brazil (45) . in 2007, a new drift resulted in influenza ah3n2 detected in south brazil (46) also affecting hospitalizations and deaths in various parts of the world (47) . we observed high rates of excess mortality in the elderly, in the years of 2003 and 2007. limitations of this study refer mainly to the ecological analysis of pooled data. we did not analyze individual information regarding comorbidities and history of vaccination that could be important confounders influencing mortality (17) . we just had the overall annual vaccination coverage which were in general, around 80% in the period. estimates of the number of deaths (all causes, respiratory, and pneumonia-influenza) supposedly related to influenza may be inaccurate in inferring the impact of respiratory viruses. correlations in time series studies may produce spurious associations, especially between all causes of death and influenza infection, due to the distance between cause and outcome, and to multiple components of the obits. serfling addresses part of this limitation by introducing sinusoidal terms in equation, since non-influenza mortality is not expected to coincide exactly with sinusoidal pattern (14, 19) . moreover, excess mortality of pneumonia, respiratory diseases, and all causes can be considered as an alert to surveillance of viral respiratory diseases, such as a sentinel indicator to be investigated (4, 48) . although all causes mortality is a non-specific indicator, it does not underestimate the complications of chronic diseases associated with influenza (4). despite the influenza component in all causes mortality is small, the indicator can be considered an indirect measure, a warning, useful in epidemiological monitoring. another limitation is the lack of robust etiologic data from virological surveillance in the years 2002-2012, which could lead to imprecision in the analyses; however, the data on the predominance strains in the southern region are reliable, and influenced the composition of the vaccine of each season. considering the option for the analysis model, serfling linear regression may produce different estimates when compared with other models (poisson, arima, and glm) (9, 10); poisson and arima models produce higher mortality estimates than serfling, and serfling higher than glm, especially among the elderly (16, 17, 21) . we chose serfling model because we do not have robust virological surveillance data, before 2013, and the study period includes a pandemic year (4) . besides, in this study, we did not analyze climatic variables (minimum temperatures and relative air humidity) that could also interfere with viral transmission and increase the impact of the disease, particularly in the elderly. in conclusion, probably previous exposures to influenza ah1n1 in the past influenced the mortality of brazilian elderly in 2009, despite the vulnerability of this age group to clinical complications. for the >70 years, we observe higher excess mortality rates (of all outcomes) in severe year of ah3n2 circulation (2003, 2007) . it is also worth noting that vaccination has been associated with the prevention of death particularly at age 65 (49) . therefore, the high elderly vaccination cover in southern brazil may have attenuated excess of mortality estimated, although the immune response is limited among those. more attention should be given to the circulation of influenza ah3n2 in subtropical regions in brazil. the reduced immune response to infection and to vaccination, and associated comorbidities recommend a special attention to this age group. besides medical assistance, the timeliness of vaccine campaigns, its composition, and etiological surveillance of respiratory diseases in the region are some of the preventive and public health measures. both authors made contributions to the conception of the work, acquisition, analysis, interpretation of data, and writing the manuscript. center for disease control and prevention. prevention and control of influenza: recommendations of the advisory committee on immunization practices (acip) influenza and the winter increase in mortality in the united states, 1959-1999 impact of respiratory virus infections on persons with chronic underlying conditions epidemiology of seasonal influenza: use of surveillance data and statistical models to estimate the burden of disease influenza-related hospitalizations among children in hong kong trends in mortality from respiratory diseases among the elderly and the influenza vaccine intervention mortality associated with influenza in tropics, state of sao paulo, brazil, from 2002 to 2011: the pre-pandemic, pandemic, and post-pandemic periods influenza-related deaths -available methods for estimating numbers and detecting patterns for seasonal and pandemic influenza in europe excess mortality associated with influenza epidemics in portugal time series methods for obtaining excess mortality attributable to influenza epidemics influenza associated mortality in the subtropics and tropics: results from three asian cities influenza in tropical regions seasonality of influenza in brazil: a traveling wave from the amazon to the subtropics methods for current statistical analysis of excess pneumonia-influenza deaths impact of influenza vaccination on seasonal mortality in the us elderly population influenza-related mortality in spain is influenza-like illness a useful concept and an appropriate test of influenza vaccine effectiveness? estimates of us influenza-associated deaths made using four different methods mortality associated with influenza and respiratory syncytial virus in the united states role of humoral and cell-mediated immunity in protection from influenza disease after immunization of healthy elderly mortality burden of the 2009 a/h1n1 influenza pandemic in france: comparison to seasonal influenza and the a/h3n2 pandemic the global circulation of seasonal influenza a (h3n2) viruses comparing clinical characteristics between hospitalized adults with laboratory-confirmed influenza a and b virus infection trends in mortality from respiratory disease in latin america since 1998 and the impact of the 2009 influenza pandemic estimated global mortality associated with the first 12 months of 2009 pandemic influenza a h1n1 virus circulation: a modelling study t cell mediated immunity to influenza: mechanisms of viral control t-cell immunity to influenza in older adults: a pathophysiological framework for development of more effective vaccines a question of self-preservation: immunopathology in influenza virus infection fatal outcome of human influenza a (h5n1) is associated with high viral load and hypercytokinemia influenza as a trigger for acute myocardial infarction or death from cardiovascular disease: a systematic review acute respiratory tract infections: a potential trigger for the acute coronary syndrome influenza and atherosclerosis: vaccination for cardiovascular disease prevention multiple immunological abnormalities in patients with type 1 (insulin dependent) diabetes mellitus use of influenza and pneumococcal vaccines in people with diabetes mortality attributable to influenza in england and wales prior to, during and after the 2009 pandemic risk factors for severe outcomes following 2009 influenza a (h1n1) infection: a global pooled analysis pandemic h1n1 influenza in brazil: analysis of the first 34,506 notified cases of influenza-like illness with severe acute respiratory infection (sari) pandemic versus epidemic influenza mortality: a pattern of changing age distribution epidemiology of influenza and its control aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus cytokine and chemokine profiles in lung tissues from fatal cases of 2009 pandemic influenza a (h1n1): role of the host immune response in pathogenesis crossreactive antibody responses to the 2009 pandemic h1n1 influenza virus the evolution of human influenza a viruses from 1999 to 2006: a complete genome study molecular evolution of human influenza a/h3n2 virus in asia and europe from 2001 to molecular characterization of influenza viruses collected from young children in uberlandia, brazil-from virus influenza detectados no estado do rio grande do sul durante center for disease control and prevention. influenza activity -united states and worldwide, 2007-08 season the impact of influenza epidemics on mortality: introducing a severity index deaths averted by influenza vaccination in the us during the seasons 2005/06 through 2013/14 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. is cited, in accordance with accepted academic practice. no use, distribution or reproduction is permitted which does not comply with these terms. key: cord-284883-bkydu285 authors: luis silva, l.; dutra, a. c.; iora, p. h.; ramajo, g. l. r.; messias, g. a. f.; gualda, i. a. p.; scheidt, j. f. h. c.; amaral, p. v. m. d.; staton, c.; rocha, t. a. h.; andrade, l.; vissoci, j. r. n. title: brazil health care system preparation against covid-19 date: 2020-05-13 journal: nan doi: 10.1101/2020.05.09.20096719 sha: doc_id: 284883 cord_uid: bkydu285 background: the coronavirus disease outbreak from 2019 (covid-19) is associated with a severe acute respiratory syndrome coronavirus 2 (sars-cov-2), a highly contagious virus that claimed thousands of lives around the world and disrupted the health system in many countries. the assessment of emergency capacity in every country is a necessary part of the covid-19 response efforts. thus, it is extremely recommended to evaluate the health care system to prepare the country to tackle covid-19 challenges. methods and findings: a retrospective and ecological study was performed with data retrieved from the public national healthcare database (datasus). numbers of intensive care unit and infirmary beds, general or intensivists physicians, nurses, nursing technicians, and ventilators from each regional health unity were extracted, and the beds per health professionals and ventilators per population rates were assessed. the accessibility to health services was also performed using a spatial overlay approach to verify regions that lack assistance. it was found that brazil lacks equity, integrity, and may struggle to assist with high complexity for the covid-19 patients in many regions of the country. conclusions: brazilian health system is insufficient to tackle the covid-19 in some regions of the country where the coronavirus may be responsible for high rates of morbidity and mortality. the coronavirus disease 2019 is associated with the novel severe acute respiratory syndrome coronavirus-2 (sars-cov-2) identified in december 2019 (1) . as of may 9, 2020, covid-19 has globally infected 4,018,342 people resulting in 278,756 deaths (2) [report 104]. the who declared covid-19 a public health emergency of international concern (pheic) by the end of january 2020 under the international health regulations (ihr) (3) . few weeks after the pheic declaration, the covid-19 outbreak was declared to be a pandemic, drawing attention worldwide (4) . the pandemic led to the adoption of several non-pharmacological interventions ranging from social distancing guidelines to national-level lockdowns by different countries (5) . these stringent interventions have severely impacted the way of living of many people and disrupted the already precarious health system in many countries (6) . in response to the covid-19 pandemic, several countries undertook analyses for the necessary health system strengthening efforts. according to studies dedicated to characterizing the clinical evolution of the disease, 39% of the cases demand emergency care, with a subset of 5% needing icu and 2.9 % demanding ventilator support to sustain life (33) . in the u.s., the percentage of patients needing ventilator support was even higher, reaching up to 12,2%. the response effort to tackle the covid-19 requires a strong organization of the emergency network (7) . the lack of beds, iniquities in the distribution of hospitals, and inadequate availability of ventilators could hamper the actions aiming to decrease the negative consequences of the covid-19 (8) . unfortunately, usually, the distribution of the health resources within the countries are characterized by inequities (9) . due to the covid-19 consequences, the scenario faced by low and medium-income countries is even more staggering (8) . the historic challenges regarding an insufficient number of health professionals, iniquities in the distribution of human resources (10) , low accessibility to emergency care services (11) , and economic issues create additional pressures to be addressed, aiming is to achieve an adequate covid-19 response. as the covid-19 spreads around the world, the hospital systems lack measures against the virus (12) , and many countries are experiencing shortages of hospital supplies (13) . for example, as of march 11, in italy, where there were 12,462 cases of covid-19 and 827 deaths, 1,028 of 5,200 beds in intensive care units (icu) are occupied. a few days later, there were no more icu beds available (14). in the united states of america, it is estimated that the disease will stress bed capacity, equipment, and health care personnel, as never seen before (15) . the brazilian case is not an exception (11) . in order to reduce the burden of covid-19, the hospital administrators, governments, policy-makers, and researchers must be prepared for a surge in the healthcare system (16) . brazil is characterized by severe social disparities and health inequities. on may 9 155,939 cases were confirmed and 10,627 deaths (17) (https://covid.saude.gov.br/). however, this number is under-reported, and the real number is estimated to be nine times greater, . 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 certified by peer review) the copyright holder for this preprint this version posted may 13, 2020. . https://doi.org/10.1101/2020.05.09.20096719 doi: medrxiv preprint according to some simulations (18) . to further the concern, the imperial college estimates that up to 1 million people will fall ill due to covid-19 in brazil (19) . during the last decade, brazil is struggling to increase the funding of the public unified system (sus). despite the efforts performed in 2016, the constitution amendment 95 (e.c. 95 acronym in portuguese) reduced the budget of the ministry of health by almost seven billion reais by year (20) . before the ec95, the brazilian health system was already underfunded (21) . two years after the ec95, the consequences regarding the lack of funding were aggravated by the covid-19 pandemic. additionally, brazil is also facing a political crisis contributing to divergences between the administrative levels in the country. the consequences of all these elements combined could hamper the response actions to tackle the covid-19. the availability of information during a crisis is essential to support the decision-making process based on evidence. taking this point into consideration the present work addresses critical aspects regarding the organization of the emergency network system in brazil, jointly with the spatial expansion of covid-19 cases within the country, and to highlight where the efforts currently performed in brazil were capable of coping with the lack of access to emergency care needed to cope covid-19 consequences. the present paper is an ecological, observational, and cross-sectional study using a spatial analysis approach. the data sources are based on secondary data from the unified health system (sus) (22) . to fulfill the defined objective, the adequacy parameters in terms of human resources, health care structure, and accessibility to emergency care services were analyzed in comparison with the reported incidence of covid-19. according to data from the brazilian institute of geography and statistics (ibge), brazil is located in south america with a territorial area of 8.510.820,623 km 2 and has a total of 210,147,125 inhabitants, with human development index (hdi) of 0.51 with diversified values for the municipalities ranging from 0.41 to 0.86 (figure 1) (23). for the assessment of methodological quality, we followed the guideline strengthening the reporting of observational studies in epidemiology (strobe). to characterize the brazilian emergency care services network, three sources were used: national register of health facilities (cnes acronym in portuguese), population data from the ibge, and covid-19 cases reported by secretariat of surveillance of the ministry of health (https://covid.saude.gov.br/). data regarding hospitals, professionals (nurses, nursing technicians, doctors, and physiotherapists), and equipment (ventilators, icu, and infirmary beds) were obtained from . 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 certified by peer review) the copyright holder for this preprint this version posted may 13, 2020. . https://doi.org/10.1101/2020.05.09.20096719 doi: medrxiv preprint the cnes website using r through the microdatasus package (24) . the population data and thematic maps were fetched from the ibge (23). the match between the number of health professionals and the recommended suitability parameters were compared using the guidelines from the national health surveillance agency (anvisa) resolution of the collegiate board of directors (rdc). the anvisa rdc number 7 provides the minimum requirements for the operation of intensive care units, in which ten icu beds are required for each one intensive care physician and one physiotherapist, one intensive care nurse for every eight beds, and two nursing assistants for each bed (25) the building of thematic maps was carried out by grouping the municipalities by health regions unity (h.r.) using software qgis 3.0. the (h.r.) is a continuous geographic space constituted by a group of bordering municipalities delimited by cultural, economic, and social identities, created by the ministry of health in order to mitigate the disparities in the country (26) . . 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 this version posted may 13, 2020. to identify regions with a high incidence of covid-19, simultaneously presenting a lack of emergency network was used as a spatial overlay approach. the first step comprised the development of an emergency infrastructure index (eii). the eii was obtained computing the number of beds registered, by the ratio of professionals and equipment according to the last competence of february 2020 from cnes. to evaluate the geographical accessibility to emergency care service care was used the two-step floating catchment area (2sfca) technique. with this approach, it was possible to assess the accessibility to emergency care services by the interaction of two geographic characteristics: (a) the volume of available hospital beds weighted by population within 2 hours of travel distance, and (b) the proximity of hospitals within a 2 hours displacement from . 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 this version posted may 13, 2020. . https://doi.org/10.1101/2020.05.09.20096719 doi: medrxiv preprint each municipality (11) . the 2sfca method generated two accessibility indexes for each municipality in brazil, one regarding the network available in february 2020, and a secondary one highlighting where the covid-19 new exclusive beds increased the access to emergency services. both indexes created the conditions to identify regions with a lack of access to emergency care, as well as the regions being benefited by the expansion of the icu beds dedicated to the codvid-19 response. to highlight regions with a high incidence of covid-19 and a lack of emergency structure, an overlap analysis was conducted to select the municipalities concurrently, showing a pattern of high incidence, jointly with a lack of access to emergency services. once the eii was computed, and the municipalities with high incidence within regions with low access to emergency care services care were identified, a getis-ord-gi analysis was performed. thus, it was possible to point out three spatial clusters: (1) emergency care services accessibility on february 20; (2) municipalities with low access to emergency care services and high covid-19 incidence, (3) accessibility to icu beds exclusively dedicated to covid-19 response in march 2020. following the resolution no. 510/16 of the national health council and considering that we used secondary sources which are available in governmental and online databases, the dispensation of the consent form was requested to the ethics committee. covid-19 has shown a fast growth rate in brazil. the total number of confirmed deaths in the country initially increased at a similar pace as germany and iran. however, differently than these countries, it has not yet shown a decrease in its growth rate ( figure 1a) . subnationally, the growth rate of confirmed deaths shows an unequal pattern. likely due to different state-level isolation policies, the states of são paulo, rio de janeiro, ceará, and amazonas have shown a much faster growth rate than the rest of the country ( figure 1b) . nonetheless, the country as a whole seems to be still far from its peak number of new deaths by covid-19. . 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 this version posted may 13, 2020. 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 this version posted may 13, 2020. february 2020) . in terms of professionals and beds per 10,000 inhabitants, the southern region had the highest rates for icu beds, ventilators, physicians, nurses, and technicians. in contrast, the northern region had the lowest ones (table 1 ). figure 2 shows the rates of beds and professionals per health regions. the icu beds per intensivist varied from zero to 53, zero to 156.5 per intensive care nurse, zero to 0.21 per technician, and zero to 2 per physiotherapist. in addition, hospital beds per physician varied from 0.10 to 7.14, 0.52 to 11.26 per nurse, 0.19 to 2.58 per technician, and 1.32 to 31.28 per physiotherapist. figure 2 shows the distribution of professionals, beds, and ventilators throughout the territory, and classifies this distribution according to rdc number 7. in a, most h.r. is by the rdc, which determines up to 10 intensivists for each icu bed. however, 132 hr do not have icu beds and / or have no intensivist. in b, only 54 h.r. are working according to the recommended amount of 1 critical care nurse for each 8 icu beds. c and d show that 322 hr are working correctly with the capacity of 1 nursing assistant and one physiotherapist for every 2 and 10 beds, respectively. in the second row of figure 1 , f, g, and h show that there are nurses, nursing technicians and physiotherapists working above the limit of 1 nurse per 8 infirmary bed, one nursing technician for each two-infirmary bed and one physiotherapist per 10 infirmary bed. . 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 this version posted may 13, 2020. panel a in figure 5 depicts the covid-19 incidence by the brazilian municipality up to 04/29/2020. it is possible to observe that all states and regions currently are presenting covid-19 cases with a highlight to the states of amazonas, amapá, espírito santo, and santa catarina, where it is already noted areas with hot colors. the hot colors indicate higher levels of incidence. in terms of deaths, all state capitals of the north, northeast, and southeast regions are presenting high levels of mortality when compared with the rest of the country. figure 6 presents three maps characterizing the brazilian situation in terms of emergency services and the covid-19 incidence. panel a exhibits the accessibility index to icu beds by population. the map highlights a higher accessibility index close to the state capitals of the brazilian states. the map b emphasizes the municipalities presenting a covid-19 incidence higher than the national average of 16.49, simultaneously with an accessibility index lower than the national mean 21 per 100,000 inhabitants thus, every municipality in the map b is facing challenges in terms of emergency care services and a high covid-19 incidence for the brazilian standards. map c presents the accessibility index of the new beds created exclusively to offer intensive care to covid-19 patients. few beds with this specific purpose were open in the states of the north and midwest region of the country. figure 7 shows the result of spatial clustering analysis to identify trends in access, as well as in the covid-19 incidence. panel a exhibits a hot spot covering the southeast, midwest, and south regions of the country. the states covered by the red layer presents the spatially significant group of municipalities with higher levels of access to icu beds by population. on the opposite side, the blue layer highlights the regions facing geographical barriers to grant access to icu beds to the population. to build the map b, the same approach was used, but this time only applied to the municipalities with high covid-19 incidence and a low index of accessibility to icu beds. the red color characterized a group of municipalities in the south and midwest regions. despite the higher availability of beds in these regions, it was possible to observe a statistically significant group of municipalities within these regions with barriers to access icu beds. map c illustrates the cluster of accessibility regarding the icu beds created to tackle the covid-19. the lack of overlay between the red color of maps b and c is pointing out a mismatch of the response efforts dedicated to addressing the covid-19 challenge. the regions in map b characterized as hotspots were considered cold spots regarding the creation of icu beds dedicated to covid-19. the result suggests that the use of scarce resources needed to put in order icu beds are not being directed to municipalities lacking access to emergency care services, despite their high levels of covid-19 incidence. the ongoing covid-19 pandemic has caused nearly 4 million confirmed cases and claimed over 278,756 lives worldwide as of may 9, 2020 (2) [report 104]. it is noteworthy to mention that the covid-19 outbreak is a challenge to the health systems worldwide (27) , and although the outcome for the crisis caused by this disease is uncertain, sars-cov-2 will overwhelm health care infrastructure for months (28) . in this study, the brazilian health system was evaluated to verify its capacity to tackle the covid-19 challenge. according to the who, it is recommended one doctor and one nurse per 1,000 inhabitants as a parameter of health care for the population (29). to strengthen the who recommendations, the brazilian health governments has established in the resolution of the collegiate board of directors number 7/2010, the quantities of icu and infirmary beds per intensivists, general physicians, nurses, nursing technician and physiotherapists (25) . although table 1 shows that in brazil, there is a sufficient number of physicians in the country, figure 1 shows that these professionals are not evenly distributed to accomplish the who recommendations and cbr. in addition, the number of nurses does not meet the criteria in the north and midwest. to illustrate the problem, figure 1 shows that brazil has desert zones of icu assistance and regions where these professionals have to take care of beds far beyond the quantities stipulated by the rdc. bahtt et al., 2017 verified that professionals in critical care that were caring for more patients per shift were more likely to experience burnout (30). halpern et al., 2017 informed that intensivists are also in shortage in the united states of america, and this situation may be attributed to burnout (31) . therefore, the combat against the covid-19 may be a difficult task in these regions, since providing access and affordable care for the large urban populations is already a challenge for many countries (32). experience from lombardia has shown that 9% of patients with covid-19 were admitted in the icu treatment, whereas this number varied from 5 to 32% in some cities in china (33) . on the other hand, in brazil, there are no available large data of icu patients at the moment, and supposing that those numbers might appear in the country as well, only 4 out of 438 health regionals could manage this number of patients. in terms of nursing care in icu accessibility, figure 1 shows that there are large regions of care voids, probably because there are low amounts of icu nurses in brazil (34) . besides that, it's possible to visualize that there are regions where icu and generalist nurses are responsible for more than eight icu and infirmary beds, which may represent a risk of unfavorable outcome for the covid-19 treatment since that high amount of patients per nurse are associated with a range of negative patient outcomes (35, 36) . the pandemic has led to severe shortages of many essential supplies, such as icu beds and ventilators (37) . based on italy's numbers that 10 to 25% of hospitalized patients will require ventilation, the centers for disease control and prevention estimates that in the usa, there will be between 1.4 to 31 patients per ventilator this period (29, 37). brazil, on the other hand, 2.5 to 3.4 million people will require hospitalization, according to the imperial . 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 this version posted may 13, 2020. college of london (19) , which represents 4 to 13 patients per ventilator if distributed equally. the numbers may represent a satisfactory amount of equipment. however, figure 1 shows that there are no ventilators in some h.r. that are potential places to have a high number of deaths. the most staggering result was obtained through the spatial cluster analysis. brazil is currently facing a double crisis. the political positioning of the president is going against the technical recommendations of the ministry of health and who. consequently, there is a disagreement between the federal administration, and the states and municipalities. on account of that situation, each administrative level is conducting several response actions against covid-19 without country-level coordination. the spatial clusters analysis highlighted that new beds created to tackle the covid-19 were misplaced. the hot spot clusters of municipalities with high incidence and lack of access are not overlapping with the hot spot cluster of new beds dedicated to the covid-19. this situation calls attention for the misplacement of scarce resources during a pandemic. the scenario depicted is the result of a lack of coordination at the national level. the consequence of misplacing the new covid-19 icu beds is an increase in the chance of deaths due to a lack of emergency care services for municipalities currently presenting a covid-19 incidence above the national average. from now on, brazil has several difficulties in treating patients in critical care. this paper shows that there is an insufficient number of icu beds, ventilators, and a huge lack of professionals in healthcare. additionally, the misplacement of the new beds aiming to fight the covid-19 pandemic contributes to worsening the situation observed through the other indicators assessed. developed countries like italy and the united states demonstrate that covid-19 can overwhelm the healthcare capacities of well-resourced nations very fast (16, 38) . therefore, the sars-cov-2 epidemic in middle-income countries, such as brazil (39), may be devastating. our findings suggest that strong leadership is needed to coordinate the response efforts against the covid-19. the limitations of this work rely on the complex data available. health data from health information systems, including health-facility records, surveys, or vital statistics, may not be representative of the entire population of a country and, in some cases, may not even be accurate (40). the cnes database presents some limitations well known by the brazilian scientific community (41) . despite this, the information regarding the availability of covid-19 beds was published just a month ago, calling attention to the occurrence of efforts aiming to improve the quality of the data available to policymakers. . 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 certified by peer review) the copyright holder for this preprint this version posted may 13, 2020. . https://doi.org/10.1101/2020.05.09.20096719 doi: medrxiv preprint a" iv to "z" ikv: attacks from emerging and re-emerging pathogens covid-19): situation report clinical characteristics of coronavirus disease 2019 in china world health organization declares global emergency: a review of the covid-19: extending or relaxing distancing control measures. lancet public health deep impact of covid-19 in the healthcare of latin america: the case of brazil communication, collaboration and cooperation can stop the 2019 coronavirus intensive care management of coronavirus disease 2019 (covid-19): challenges and recommendations global surgery 2030: evidence and solutions for achieving health, welfare, and economic development addressing inequalities in medical workforce distribution: evidence from a quasiexperimental study in brazil addressing geographic access barriers to emergency care services: a national ecologic study of hospitals in brazil universal masking in hospitals in the covid-19 era fangcang shelter hospitals: a novel concept for responding to public health emergencies how should u.s. hospitals prepare for coronavirus disease 2019 (covid-19)? covid-19): update for anesthesiologists and intensivists the immune escape mechanisms of mycobacterium tuberculosis comparison of the microwave-heated ziehl-neelsen stain and conventional ziehl-neelsen method in the detection of acid-fast bacilli in lymph node biopsies. open access maced the global impact of covid-19 and strategies for mitigation and suppression. imperial college covid-19 response team emenda constitucional 95/2016 e o teto dos gastos públicos: brasil de volta ao estado de exceção econômico e ao capitalismo do desastre implicações de decisões e discussões recentes para o financiamento do sistema único de saúde. saúde em debate regulamenta a lei no 8.080, de 19 de setembro de 1990, para dispor sobre a organização do sistema único de saúde-sus, o planejamento da saúde, a assistência à saúde ea articulação interfederativa, e dá outras providências microdatasus: pacote para download e préprocessamento de microdados do departamento de informática do sus (datasus). cadernos de saúde pública dispõe sobre os requisitos mínimos para funcionamento de unidades de terapia intensiva e dá outras providências brasília região de saúde e suas redes de atenção: modelo organizativo-sistêmico do sus. ciência & saúde coletiva covid-19: operational guidance for maintaining essential health services during an outbreak: interim guidance world health o. health workforce requirements for universal health coverage and the sustainable development goals.(human resources for health observer, 17). 2016. 30 critical care medicine in the united states: addressing the intensivist shortage and image of the specialty organizational characteristics, outcomes, and resource use in 78 brazilian intensive care units: the orchestra study baseline characteristics and outcomes of 1591 patients infected with sars-cov-2 admitted to icus of the lombardy region profile of an intensive care nurse in different regions of brazil ratios and nurse staffing: the vexed case of emergency departments workloads in australian emergency departments a descriptive study the toughest triage -allocating ventilators in a pandemic hospital surge capacity in a tertiary emergency referral centre during the covid-19 outbreak in italy factors potentially associated with the decision of admission to the intensive care unit in a middle-income country: a survey of brazilian physicians. rev bras ter intensiva cadastro nacional de estabelecimentos de saúde: evidências sobre a confiabilidade dos dados. ciênc. saúde coletiva [internet] we would like to thank the coordination for the improvement of higher education personnel (capes). the authors declare no conflicts of interest. . 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 this version posted may 13, 2020 key: cord-292209-d1ty9etr authors: horta, bernardo l; silveira, mariângela f; barros, aluísio j d; barros, fernando c; hartwig, fernando p; dias, mariane s; menezes, ana m b; hallal, pedro c; victora, cesar g title: prevalence of antibodies against sars-cov-2 according to socioeconomic and ethnic status in a nationwide brazilian survey date: 2020-10-29 journal: rev panam salud publica doi: 10.26633/rpsp.2020.135 sha: doc_id: 292209 cord_uid: d1ty9etr objectives. to investigate socioeconomic and ethnic group inequalities in prevalence of antibodies against sars-cov-2 in the 27 federative units of brazil. methods. in this cross-sectional study, three household surveys were carried out on may 14-21, june 4-7, and june 21-24, 2020 in 133 brazilian urban areas. multi-stage sampling was used to select 250 individuals in each city to undergo a rapid antibody test. subjects answered a questionnaire on household assets, schooling and self-reported skin color/ethnicity using the standard brazilian classification in five categories: white, black, brown, asian or indigenous. principal component analyses of assets was used to classify socioeconomic position into five wealth quintiles. poisson regression was used for the analyses. results. 25 025 subjects were tested in the first, 31 165 in the second, and 33 207 in the third wave of the survey, with prevalence of positive results equal to 1.4%, 2.4%, and 2.9% respectively. individuals in the poorest quintile were 2.16 times (95% confidence interval 1.86; 2.51) more likely to test positive than those in the wealthiest quintile, and those with 12 or more years of schooling had lower prevalence than subjects with less education. indigenous individuals had 4.71 (3.65; 6.08) times higher prevalence than whites, as did those with black or brown skin color. adjustment for region of the country reduced the prevalence ratios according to wealth, education and ethnicity, but results remained statistically significant. conclusions. the prevalence of antibodies against sars-cov-2 in brazil shows steep class and ethnic gradients, with lowest risks among white, educated and wealthy individuals. in brazil, prominent covid-19 cases, including state governors and more recently president jair bolsonaro (https://www. bbc.com/news/world-latin-america-53319517), led to a disseminated impression that the epidemic affects brazilian society as a whole, without distinction of class or ethnic group. if true, this finding would be in sharp contrast with data from high-income countries, where the pandemic is disproportionally affecting ethnic minorities and poor populations (1) . in the united states (https://www.nytimes.com/interactive/2020/07/05/ us/coronavirus-latinos-african-americans-cdc-data.html), african-americans and latinos are suffering from higher disease incidence and mortality than whites, according to reported cases. a study carried out in the oxford royal college of general practitioners research and surveillance centre network observed that black people and those living in the more deprived areas were more likely to test positive for sars-cov-2 (2) . another study in the united kingdom (3) reported that non-white ethnicity and higher deprivation scores were strongly associated with increased covid-19 mortality. in contrast, the large national surveys carried out in spain did not find either nationality or education as risk factors for the presence of antibodies against sars-cov-2 (4). we were only able to locate a single study of ethnic or social inequalities in covid-19 in low-or middle-income countries. baqui et al (5) described that in brazil, covid-19 hospital case-fatality was higher among individuals classified with black or with mixed ancestry, compared to whites (5) . a commentary on this publication argued, without providing new data, that living conditions of brazil's poor would make them more vulnerable to covid-19 morbidity and mortality (6) . their study did not include a sufficient number of indigenous individuals for analyses. we were unable to locate any population-based study from low or middle-income countries on social and ethnic inequalities in covid-19 morbidity or mortality. the present analyses were aimed at assessing socioeconomic and ethnic group inequalities in prevalence of antibodies against sars-cov-2 in 133 sentinel cities throughout brazil, as part of the epicovid-19 study (www.epicovid19brasil.org). in this cross-sectional study, three population-based repeated serological surveys were carried out in 133 brazilian sentinel cities in brazil's 27 federative units. the cities included brasilia, 26 state capitals and the largest cities in each of the country's intermediate regions, as defined by the brazilian institute of geography and statistics (ibge). in each city, 25 urban census tracts were selected with probability proportionate to size, and 10 households were randomly sampled in each tract. in each sampled household, all residents were listed, and one was randomly selected to be tested. if the selected individual refused to provide a blood sample, a second household member was randomly selected. if this person also refused, the interviewers moved on to the next household to the right of the one that had been originally selected. the next household to the right was also selected in case of absent residents. in the present manuscript, we pooled the data from the three survey waves that took place on may 14-21, june 4-7, and june 21-24, 2020. with 250 individuals per city, the margins of error (approximately two standard errors) for estimating prevalence figures of 2%, 5% and 10% are respectively 1.77, 2.70, and 3.79 percent points, and at national level, with total sample size of 33 250, the corresponding margins of error are 0.15, 0.24 and 0.33. the wondfo sars-cov-2 antibody test (wondfo biotech co., guangzhou, china) was used to evaluate the presence of antibodies for sars-cov-2, using finger prick blood samples. at the time of the first survey, this was the only test available in the country in large numbers, and over 100 000 tests were provided to the study by the ministry of health. the test detects immunoglobulins of both igg and igm isotypes specific to sars-cov-2 antigens in a lateral flow assay. the assay reagent consists of colloidal gold particles coated with recombinant sars-cov-2 antigens. following the introduction of the blood sample, reactive antibody:antigen:colloidal gold complexes, if present, are captured by antibodies against human igm and igg present on the "test" (t) line in the kit's window, leading to the appearance of a dark-colored line. valid tests are identified by a positive control line (c) in the same window. if this control line is not visible, the test is deemed non-conclusive, which is uncommon. the rapid test underwent independent validation studies that used rt-pcr as the gold standard. according to the manufacturer, it has a sensitivity of 86.4% and specificity of 99.6% (https://en.wondfo.com.cn/product/wondfo-sars-cov-2-antibody-test-lateral-flow-method-2/). a validation study carried out by the national institute for quality control in health (incqs, oswaldo cruz foundation, rj, brazil) showed a sensitivity of 100% and specificity of 98.7%. whitman et al evaluated 10 different lateral flow assays (7) and reported that the wondfo test had a sensitivity of 81.5% and specificity of 99.1%. a validation study carried out by our research group observed a sensitivity of 77.1% and specificity of 98.0% (8) . by pooling the results from the four validation studies, weighted by sample sizes, sensitivity is estimated at 84.8% (95% ci 81.4%;87.8%) and specificity at 99.0% (95% ci 97.8%; 99.7%) (8) . participants answered short questionnaires including sociodemographic information (sex, age, schooling, skin color, household size and household assets), covid-19-related symptoms, use of health services, compliance with social distancing measures and use of masks. due to the presence of widespread multiethnic population, the official brazilian classification of ethnicity recognizes five groups, based on the question: "how do you classify yourself in terms of color or race?" the five response options are "white", "brown" ("pardo" in portuguese), "black", "yellow (asian)" and "indigenous". interviewers were instructed to check the "yellow" option when the respondent mentions being of asian descent, and "indigenous" when any of the multiple first nations are mentioned. the "brown" category reflects mixed ancestry including european, african and/or indigenous backgrounds. this system is endorsed by the afro-descendants movement, which advocates for disaggregation of all national statistics to raise their visibility (9) . socioeconomic position was assessed using a wealth index derived through principal component analyses of household assets (10). the first component was divided into quintiles. achieved schooling was recorded as the highest grade completed successfully. field workers used tablets to record the full interviews, register all answers, and photograph the test results. the questionnaire was applied before the test result was disclosed to each participant. inconclusive tests were repeated, and 35 subjects presented a non-conclusive result in the second test, which were treated as missing values. all positive or inconclusive tests were read by a second observer, as well as 20% of the negative tests. five regions of the country. in these analyses, the prevalences of seropositivity were still lower in the richest quintile, but the magnitude of the prevalence ratio decreased. indigenous individuals still showed higher prevalence than whites (prevalence ratio: 2.25; 95% ci 1.74; 2.91), as did individuals classified as black or brown. table 3 shows that in the northern region, in spite of the decrease in the magnitudes of the associations compared to the national analyses (table 2) , the inverse associations with wealth remained significant, and the higher prevalence among indigenous and brown subjects compared to whites also persisted. in the northeastern region, seroprevalence was also inversely associated with wealth, but not with ethnicity. prevalence for indigenous subjects were 2.27 times higher than for whites. in the remaining regions, where prevalence was low at the time of the surveys, we did not observe any clear pattern of association with wealth, but black and brown subjects had significantly higher risks than whites. consistent results were observed for education in all regions, with lower risk for subjects with 12 or more years of schooling than for the other groups. table 4 shows that the even after controlling for region and socioeconomic status, the seroprevalence remained significantly higher among indigenous, brown and black subjects. interviewers were tested and found to be negative for the virus and were provided with individual protection equipment that was discarded after visiting each home. we used stata 15 for the analyses. proportions of positive tests according to region, sex, wealth quintiles, achieved schooling and skin color were compared using the chi-squared test. for ordinal variables, both in bivariate and multivariate analyses, we estimated the p-value for linear trend and for heterogeneity, and presented the one with the lower p-value. we also stratified the analyses of seroprevalence according to socioeconomic variables by region of the country (north; northeast; southeast; south and center-west), using poisson regression with robust variance to estimate prevalence ratios. all analyses controlled for the cluster-sampling design using svy prefix. ethical approval was obtained from the brazilian's national ethics committee (process number caae 30721520.7.1001.5313), with written informed consent from all adult participants; for minors, written consent was provided by parents or caregivers, and assent forms were also signed by the child or adolescent (provided that they were literate). the dataset is stored in anonymous form. positive cases were reported to the municipal covid-19 surveillance systems. in the three waves of the seroprevalence survey, 89 397 subjects were tested and 35 individuals with inconclusive test results in the test and retest were excluded from the analyses. therefore, in the present study we evaluated 89 362 subjects. the response rates were 54.4%, 52.6% and 55.6% in the three waves, mainly due to the fact that the whole family was away from home when the visit took place. the prevalence of positive results was 1.4%, 2.4%, and 2.9% in the first, second and third surveys, respectively. table 1 shows that the proportion of males and young subjects in the studied population was below what was expected on the basis of the national population. concerning skin color, most of the studied subjects reported being mixed (brown) or white and only 1.4% self-identified as indigenous. the proportion of subjects who reported being white was lower than the national estimates. in the three phases of the study, there were 2 064 positive tests (2.31%) among the 89 362 subjects with valid test results. table 2 shows that the proportion of positive tests was higher in the north region (6.7%), whereas in the southern region only 0.2% of the studied subjects had a positive test. results for unadjusted analyses, and analyses with adjustment for age and sex, were very similar. antibody prevalence was inversely associated with wealth quintiles; compared to the wealthiest, the poorest were about twice as likely to present antibodies against sars-cov-2. for schooling, the association was not linear, but subjects with 12 or more years of schooling were less likely to present positive tests than any of the other groups. the largest prevalence ratio were observed in the comparison between indigenous and white individuals, with a near five-fold ratio. whites were less likely to test positive than any ethnic group, followed by asians. because the proportion of individuals with antibodies against sars-cov-2 was higher in the northern (amazon) region, where indigenous and poor populations are concentrated, we carried out additional analyses with further adjustment for the our study is the largest population-based serological survey for antibodies against sars-cov-2 in low-and middleincome countries, and only comparable to the national surveys carried out in spain (4). our findings show that the covid-19 pandemic is hitting harder at the poorest and disadvantaged groups in brazil. the proportions of individuals with positive tests was higher among indigenous, black and brown subjects compared to whites, as well as being inversely associated with socioeconomic position. concerning ethnic inequalities in health and nutrition in brazil, several studies have reported that indigenous children and adolescents show higher mortality than other ethnic with respect to the study limitations, the use of rapid serological tests for clinical decision-making and for defining individuals as immune to covid-19 has been criticized. but the use of such tests to estimate the seroprevalence is much less controversial, provided the test has been validated (16, 17) . the rapid test used in our study (wondfo sars-cov-2 antibody test) underwent different validation studies using rt-pcr as the gold standard, including one carried out by our own team. these studies estimated the test's sensitivity and specificity at 84.8% and 99.0%, respectively. it has been suggested that using capillary blood to estimate seroprevalence tends to increase the rate of false negative results (18) ; however, this finding has not been replicated by other studies (19) . furthermore, our validation study (8) used capillary blood and the observed sensitivity was similar to that reported in another studies. therefore, this should not be considered as a main study limitation as all population subgroups should be affected. recent evidence suggests that antibody levels against sars-cov-2 fall rapidly over a few weeks, regardless of the type of test used (20) ; therefore, our results correspond to relatively recent infections rather than cumulative prevalence. again, all population subgroups are likely to be similarly affected. the restriction of the sample to sentinel sites that are the larger and more developed cities should not be considered as a major limitation, as we are not trying to estimate the prevalence of the infection in the whole country, but its association with socioeconomic and demographic characteristics. due to logistic difficulties including a massive fake news campaign through social media, it was not possible to complete the first round of the study in 87 cities, so that the sample size was 25 025 instead of the planned 33 250 tests. these difficulties were overcome in the next two rounds, when the intended sample size was nearly achieved. concerning selection bias, the response rates of around 54% are similar to that reported in the spanish survey (59.5%) and higher than achieved in national surveys in iceland and austria, both of which had response rates of about one third of the intended sample (21) . the higher proportion of female in the studied sample could be due to the fact that males were less like to comply with the stay at home recommendations. the most frequent reason for non-response was the fact that the whole family was away from home when the visit took place, which may be associated with temporary moves to smaller towns or to rural area, as larger cities were more strongly hit by the pandemic in the early phases. regarding indigenous populations, it should be noted that our sample was restricted to those living in urban areas. lastly, our sample had fewer children than expected, which was probably due to their reluctance to undergo a finger prick when randomly selected within the household; in these cases, a second person was randomly selected and if that person also refused the household was replaced. in summary, the analyses of the three waves of national serological surveys in brazil showed important inequalities in the prevalence of antibodies against sars-cov-2 according to family wealth, education and ethnic groups. contrary to the initial impressions that covid-19 would strike all groups in brazilian society with similar intensity, our analyses show that individuals from poor families and with little schooling were at higher risk of having been infected. in terms of ethnicity or skin color, whites had the lowest risk, whereas indigenous subjects and those with black or brown skin color were most affected (22) . groups (11) , and that similar gaps are also observed for adult mortality (12) . indeed, there is overwhelming evidence that indigenous populations have been left behind when health conditions improved in brazil in the recent past (13) . it would be surprising if covid-19 turned out to be different from other existing health conditions. it has been reported that covid-19 is hitting hard at rural indigenous villages in reservations (14) , but there are no comparisons with other ethnic groups. as mentioned in the introduction, baqui et al (5) found that covid-19 hospital case-fatality was higher among individuals classified with black and with mixed ancestry, compared to whites. this study was based on a public dataset on hospitalizations and only a few subjects were identified as indigenous, and for this reason the case fatality among them was not estimated (5) . because the magnitude of the association of seroprevalence for covid-19 and skin color decreased after controlling for region of the country, the five-fold difference observed in antibody prevalence between indigenous and white subjects had been partly inflated by place of residence. yet, even after adjustment for region, indigenous individuals were about twice as likely as whites to present antibodies against sars-cov-2, and in the national analyses including adjustment for region of the country and socioeconomic status, the prevalence ratio remained at around two. the interpretation of these analyses suggests that indigenous subjects were at substantially higher risk than other ethnic groups. this was partly due to the fact that they were concentrated in the amazon region, where prevalence was the highest in the country at the time of the surveys, and also because their living standards were the lowest when compared to other groups. nevertheless, their increased risk persisted in the stratified and adjusted analyses for socioeconomic status. future studies will need to investigate the mechanisms behind this association. in terms of ethnicity, the "brown" or "pardo" category had the second highest prevalence among the five groups. this category includes individuals who self-report has having mixed ancestry. genomic ancestry studies (15) show that in the northern city of belém self-classified brown individuals had, on average, 69% european ancestry, followed by 21% amerindian ancestry and 11% african ancestry, while in the south they had on average 44% european, 11% amerindian and 45% african ancestries. therefore, the evidence suggests that brown subjects in the north -among whom seroprevalence was 7.1%-were genetically closer to amerindians than was the case for the same group in other parts of the country. sponsors did not influence in any way the design, the data collection, the analysis, the writing, and the decision to publish these results. prevalencia de anticuerpos contra el sars-cov-2 según el estatus socioeconómico y étnico en una encuesta nacional de brasil resumen objetivos. investigar las desigualdades socioeconómicas y entre distintos grupos étnicos en la prevalencia de anticuerpos contra el sars-cov-2 en las 27 unidades federativas del brasil. métodos. en este estudio transversal, se realizaron tres encuestas de hogares los días 14-21 de mayo, 4-7 de junio y 21-24 de junio, 2020 en 133 áreas urbanas brasileñas. se utilizó un muestreo de etapas múltiples para seleccionar 250 individuos en cada ciudad a fin de someterlos a una prueba rápida de anticuerpos. los sujetos respondieron un cuestionario sobre los bienes del hogar, la escolaridad y el color de la piel/etnia (autodeclarado utilizando la clasificación brasileña estándar de cinco categorías: blanco, negro, pardo, asiático o indígena). se utilizó el análisis de los componentes principales de los bienes para clasificar la posición socioeconómica en cinco quintiles de riqueza. se empleó la regresión de poisson para los análisis. resultados. se analizaron 25 025 sujetos en la primera encuesta, 31 165 en la segunda y 33 207 en la tercera, que mostraron una prevalencia de resultados positivos de 1,4%, 2,4% y 2,9% respectivamente. los individuos del quintil más pobre tuvieron 2,16 veces más probabilidades de presentar un resultado positivo (intervalo de confianza del 95% 1,86; 2,51) que los del quintil más rico, y los que tenían 12 o más años de escolaridad tuvieron una prevalencia menor que los sujetos con menos educación. las personas indígenas presentaron una prevalencia 4,71 (3,65; 6,08) veces mayor que las blancas, al igual que las de piel negra o parda. el ajuste por región del país redujo los índices de prevalencia según la riqueza, la educación y el origen étnico, pero los resultados siguieron siendo estadísticamente significativos. conclusiones. la prevalencia de anticuerpos contra el sars-cov-2 en el brasil muestra gradientes relacionados con la posición socioeconómica y la etnia muy pronunciados, con menor riesgo en las personas blancas, educadas y ricas. epidemiología; infecciones por coronavirus; encuestas y cuestionarios; inequidad social; brasil. objetivos. investigar as desigualdades socioeconômicas e étnicas na prevalência de anticorpos contra sars-cov-2 nas 27 unidades federativas do brasil. métodos. neste estudo transversal, três pesquisas domiciliares foram realizadas de 14 a 21 de maio, 4 a 7 de junho, e 21-24 de junho, 2020 em 133 áreas urbanas brasileiras. amostragem em várias etapas foi utilizada para selecionar 250 indivíduos em cada cidade para se submeter a um teste rápido de anticorpos. os sujeitos responderam a um questionário sobre bens domésticos, escolaridade e cor da pele/etnicidade (auto-relatada utilizando a classificação padrão brasileira de cinco categorias: branco, preto, pardo, asiático ou indígena). a análise dos componentes principais dos ativos foi utilizada para classificar a posição socioeconómica em cinco quintis de riqueza. a regressão de poisson foi utilizada para as análises. resultados. 25 025 indivíduos foram testados na primeira pesquisa, 31 165 na segunda, e 33 207 na terceira, com prevalência de resultados positivos de 1,4%, 2,4% e 2,9%, respectivamente. indivíduos no quintil mais pobre tinham 2,16 vezes (intervalo de confiança de 95% 1,86; 2,51) mais probabilidade de ter um resultado positivo do que aqueles do quintil mais rico, e aqueles com 12 ou mais anos de escolaridade tinham uma prevalência menor do que aqueles com menos educação. os indivíduos indígenas tinham 4,71 (3,65; 6,08) vezes mais prevalência do que os brancos, assim como aqueles com cor da pele preta ou parda. o ajuste regional reduziu as taxas de prevalência de acordo com a riqueza, educação e etnia, mas os resultados permaneceram estatisticamente significativos. conclusões. a prevalência de anticorpos contra a sars-cov-2 no brasil mostra gradientes relacionados com a posição socioeconómica e a etnia muito acentuados, com os menores riscos entre os indivíduos brancos, educados e ricos. society and the slow burn of inequality risk factors for sars-cov-2 among patients in the oxford royal college of general practitioners research and surveillance centre primary care network: a cross-sectional study opensafely: factors associated with covid-19 death in 17 million patients prevalence of sars-cov-2 in spain (ene-covid): a nationwide, population-based seroepidemiological study ethnic and regional variations in hospital mortality from covid-19 in brazil: a cross-sectional observational study in the covid-19 pandemic in brazil, do brown lives matter? lancet glob health test performance evaluation of sars-cov-2 serological assays sensitivity and specificity of a rapid test for assessment of exposure to sars-cov-2 in a community-based setting in brazil características étnico-raciais da população: classificação e identidades a nationwide wealth score based on the 2000 brazilian demographic census differences in mortality between indigenous and non-indigenous persons in brazil based on the 2010 population census indigenous children and adolescent mortality inequity in brazil: what can we learn from the 2010 national demographic census? emerging health needs and epidemiological research in indigenous peoples in brazil covid-19 experience among brasil s indigenous people the genomic ancestry of individuals from different geographical regions of brazil is more uniform than expected serology for sars-cov-2: apprehensions, opportunities, and the path forward the role of antibody testing for sars-cov-2: is there one? sensitivity of the wondfo one step covid-19 test using serum samples analytical performance of lateral flow immunoassay for sars-cov-2 exposure screening on venous and capillary blood samples rapid decay of anti-sars-cov-2 antibodies in persons with mild covid-19 spread of sars-cov-2 in the icelandic population health conditions and health-policy innovations in brazil: the way forward disclaimer. authors hold sole responsibility for the views expressed in the manuscript, which may not necessarily reflect the opinion or policy of the rpsp/pajph and/or paho.authors´ contributions. blh, mfs, pch, cgv conceived the study, analyzed the data, wrote/reviewed the manuscript. ajdb, fcb, fph, msd, ambm contributed with data analysis, interpreted the results, and reviewed the manuscript. all authors reviewed and approved the final version.funding. the study was funded by the brazilian ministry of health, instituto serrapilheira, brazilian collective health association and the jbs sa initiative fazer o bem faz bem. the key: cord-102490-yvcrv94c authors: souza, jonatas s. de; abe, jair m.; lima, luiz a. de; souza, nilson a. de title: the general law principles for protection the personal data and their importance date: 2020-09-29 journal: nan doi: 10.5121/csit.2020.101110 sha: doc_id: 102490 cord_uid: yvcrv94c rapid technological change and globalization have created new challenges when it comes to the protection and processing of personal data. in 2018, brazil presented a new law that has the proposal to inform how personal data should be collected and treated, to guarantee the security and integrity of the data holder. the purpose of this paper is to emphasize the principles of the general law on personal data protection, informing real cases of leakage of personal data and thus obtaining an understanding of the importance of gains that meet the interests of internet users on the subject and its benefits to the entire brazilian society. the concern about the protection of people's data has grown over the years, but only after the approval of the brazilian law that received the name of marco civil da internet, established by law no. 12,965, 2014 [1] . in brazil, a new law has recently been sanctioned and it is generating a lot of discussion in several areas. the general law on personal data protection, law no. 13.709 [2] of 14 th august 2018, gives the brazilian population rights and guarantees on how organizations will have to adapt to the collection and processing of personal data, whether by physical or digital means. discussing data protection in brazil has become a challenging task. the state of the crisis provoked by covid-19 (coronavirus) had a severe impact on companies, which began to adopt measures to make their workforce compatible with the demands existing during social isolation, and the adoption of measures to minimize the risk of the disease spreading among their workforce. the use of virtual private network -vpn and practices such as byod (bring your own device) have become common to incorporate daily life. there was also an exponential growth of e-commerce, home office, webinars, virtual meetings, and numerous activities that started to occur entirely through the internet. in the same proportion, the risks associated with the improper use of personal data, data leaks, improper access by third parties, theft of data kept by corporate servers, creation of fake profiles, fake news, among other practices frequently reported were multiplied. the objective of the paper is to present important aspects such as the principles and fundamentals of brazilian law and to present some real cases on data leaks. the paper is composed of sections, in section 2 presents the theoretical reference that will address the history of data protection in brazil and the european regulation, in section 3 describes the principles of brazilian law demonstrating the similarity with the european regulation, in section 4 the importance of brazilian law showing the fundamentals of the law and emphasizes the importance of consent of the data holder, in section 5 the results and discussions with real cases of data leaks and countries that already have some legislation on protection of personal data, in section 6 are the conclusions bringing the final considerations obtained. in brazil, the legislation is based on the positivist model of law, adopted by lusitanian, german and italian schools that privilege the written law, this reflects in the delay of the implementation of the legislative process (figure 1), which begins with the initial idea, passes through the creation of the bill, then through the bicameral approval and then the presidential sanction, to finally come into force with coercive force. the first brazilian initiative on personal data protection was in article 5 of the 1988 federal constitution [3] . art. 5 all are equal the law, without distinction of any nature, guaranteeing brazilians and foreigners residing in the country the inviolability of the right to life, freedom, equality, security, and property, under the following terms [3] : x -the intimacy, privacy, honor, and image of persons are inviolable, and the right to compensation for material or non-material damage resulting from their violation is guaranteed [3] . xii -the secrecy of correspondence and telegraphic communications, data, and telephone communications shall be inviolable, except in the latter case by judicial order, in the cases and the manner established by law for criminal investigation or criminal proceedings [3] . law no. 9.296, of july 24th, 1996 [4] deals with the interception of telephone communications and regulates clauses xii, art. 5 of the federal constitution. on september 11th, 1990 [5] law no. 8.078, known as the consumer code (cdc), was enacted, bringing in its article 43 the guarantee of access to the holder's data, demanding clarity and objectivity of the information and the possibility for the consumer to demand the correction of his registration data [5] . art. 43 the consumer, without prejudice to the provisions of art. 86, shall have access to the information existing in registers, files, records, personal data, and consumption filed about him, as well as to their respective sources [5] . paragraph 1. consumer registrations and data must be objective, clear, truthful, and in easy-tounderstand language, and may not contain negative information for a period longer than five years [5] . paragraph 2. the opening of the registration, file, record, personal, and consumption data shall be communicated in writing to the consumer when not requested by him [5] . paragraph 3. the consumer, whenever he finds any inaccuracy in his data and registrations, may demand their immediate correction, and the archivist shall, within five working days, communicate the change to the eventual recipients of the incorrect information [5] . paragraph 4. databases and registers relating to consumers, credit protection services, and the similar are considered public entities [5] . paragraph 5. once the statute of limitations on the collection of consumer debts has been consummated, the respective credit protection systems shall not provide any information that may prevent or hinder new access to credit with suppliers [5] . paragraph 6. all information referred to in the caption of this article must be made available in accessible formats, including for persons with a disability, at the request of the consumer [5] . even bringing some progress on personal data protection, the cdc was still limited in its scope on the subject, which means that the protection would exist in the relationship between supplier and consumer within the scope of the legal concepts established in articles 2 and article 3 [5] of the cdc. on april 23rd, 2014, law no. 12,965, now known as marco civil da internet [1] , was approved, establishing principles, guarantees, rights, and duties for the use of the internet in brazil, and has the guarantee of privacy and protection of personal data, and will only make such data available through a court order. in art. 7, clauses i, ii and iii, and clauses vii, viii, ix, and x, deal with the rights of the holders of personal data [1] . art. 7 access to the internet is essential to the exercise of citizenship, and the user has assured the following rights [1] : i -inviolability of intimacy and privacy, their protection and compensation for material or moral damage resulting from their violation [1] . ii -inviolability and secrecy of the flow of your communications over the internet, except by court order, in the form of the law [1] . iii -inviolability and secrecy of your stored private communications, except by court order [1] . vii -do not provide third parties with your data, including connection records, and access to internet applications, except by free, express and informed consent or in the cases provided by law [1] . viii -clear and complete information about the collection, use, storage, treatment and protection of your data, which may only be used for purposes that: a) justify their collection; b) are not prohibited by law, and c) are specified in service contracts or terms of use of internet applications [1] . ix -express consent on the collection, use, storage, and processing of personal data, which shall occur in a manner detached from the other contractual clauses [1] . x -definitive exclusion of personal data that you have provided to a certain internet application, at your request, at the end of the agreement between the parties, except for the cases of mandatory storage of records provided for in this law [1] . the civil framework of the internet also includes aspects of the responsibility for the protection of personal data by access providers and in operations carried out through the internet, providing for some sanctions, described in articles 10, 11, and 12 [1] . on august 4th, 2018, law no. 13,709, called the general law on personal data protection [6] , was approved, providing for the processing of personal data, whether digital or not, to protect the fundamental rights of freedom and privacy and the development personal personality of the individual in society. the general law on personal data protection -lgpd, law no. 13.709 of 14th august 2018, which would come into force in august 2020, has been postponed by provisional measure no. 959/2020 [6] extending the vacatio legis [7] and postponed to 3 may 2021 [8] . the lgpd purpose is to provide guidelines on how personal data will be collected and processed, and to ensure the security and integrity of the data holder, whether digital or not. on 10th july 2018, project law 53/2018 -plc [9] was approved by the plenary of the federal senate and was sanctioned on 14th august 2018 by the 37th president of brazil [2] . article 1 of the lgpd states that it is prepared to protect the processing of personal data to protect the rights of freedom, privacy, and personality development of the individual. moreover, it applies to any individual or legal entity that carries out-processing operations such as collection, production, reception, classification, processing, among other activities by physical or digital means in brazilian territory, or abroad if it is using personal data of individuals living in brazil. the general data protection regulation 2016/679 [10] -gdpr, of the european parliament and of the council of european union -eu, of 27th april 2016, is a regulation that is on the protection of individuals about the processing of personal data and the free movement of such data and that repeals directive 95/46/ec [11] , eu companies had two years to comply with the regulation by the date of 28th may 2018. the regulation applies to all activities involving the processing of personal data using full or partial consent, as well as to the processing of personal data by non-automated means. for a better understanding of lgpd [2] , it is necessary to know the legal bases (principles) that should be observed for any type of data processing activities, the law is composed of ten principles that are listed in art 6. a gdpr [10] [12] is also guided by principles [13] , which are set out in article 5, which form the basis for the eu regulation, and these principles should be linked to data processing. the lgpd [2] , the purpose for which the data will be done must be very specific, explicit, and informed to the holder of the personal data that will be processed [2] . in gdpr, the purpose limitation principle [13], the data must be collected for specific, legitimate, and explicit purposes, and may not be processed for other unspecified purposes [10] . the lgpd [2] , is the formality with the holder of the personal data to process personal data [2] . in gdpr, the storage limitation principle [13], data may be stored in a database until the end of the data processing and must be informed to the data owner, and after the end of the processing, the data must be deleted from the database. it is also linked to the principle of bidding [13] that the company that will process the data must comply with the regulation and with the data holder. [10]. in the lgpd [2] , the amount of data for data processing is only relevant, proportional, and not excessive [2] . in the european regulation, the data minimization principle [13], data should be collected following its purpose and only data that are necessary for the processing [10] . the lgpd [2] , guarantees that the data holder will have free access to the data in its entirety at any time, and this principle is linked to the gdpr transparency principle. in the european regulation there is a right which is described in article 17 [10] , which is called right to erasure [10] or right of forgetfulness, which gives the "right to be forgotten" to the data holder of the database concerning the purpose of the processing, after the data holder has requested to delete the data, the officer shall delete the data relating to the data holder's request [10] . the lgpd [2] , guarantees the data owner clarity, accuracy, and relevance and updates the data according to the needs of the data treatment [2] . the accuracy principle of gdpr [13] that data should always be updated and correct thus maintaining the quality of the data that will be processed and incorrect data will be rectified or deleted [10] . the lgpd [2] , ensures that the data owner will have access to all necessary information clearly, accurately, and easy access to data processing [2] . the transparency principle of gdpr is divided into three words, lawfulness, fairness, and transparency [10] [13]. the lawfulness or bidding is concerned, data controllers should comply with the regulation, on fairness or loyalty, it is stated that processing should take place fairly with the consent of the data owner, and on transparency, the data controller will allow him to have access to all information of the data processing [10] . the lgpd [2] , will use techniques for the protection of personal data from unauthorized access or accidental or illicit situations of alteration, destruction, loss, dissemination, and communication [2] . the principle that about security in gdpr is the integrity principle and confidentiality [13], the data must be stored securely, guaranteeing the data integrity, and adopting methods of protection against unauthorized processing, loss, accidental damage, destruction, or unauthorized access [10] . it will use methods to prevent data processing damaging [2] [10]. data may not be processed for discrimination, illicit or abusive purposes [2] . in brazilian law [2] , it is up to the treatment agent to prove the purpose and which effective methods have been adopted, and he must be able to prove compliance with and enforcement of personal data protection rules, including the effectiveness of these methods [2] . in the european regulation, the accountability principle [13] , which is the full responsibility of the data processing agent, guarantees the length of the purpose of the processing and has evidence of the necessity of the processing [10] . the lgpd [2] , sanctioned in brazil, was inspired by gdpr of the eu [10] and contains many similarities in its respective principles. in its art. 2 they show the foundations (figure 2), that served as a basis for the development of the law [2] : art. 2 the discipline of personal data protection based on the according to fundamentals [2] : i -respect for privacy [2] . ii -informative self-determination [2] . iii -freedom of expression, information, communication, and opinion [2] . iv -the inviolability of intimacy, honour, and image [2] . v -economic and technological development and innovation [2] . vi -free enterprise, free competition, and consumer protection [2] . vii -human rights, free development of personality, dignity, and the exercise of citizenship by natural persons [2] . one of the most important points that makes data processing possible is to have the consent of the data holder, according to article 7, clauses 1 [2] , and in article 8 [2] it is reinforced that the authorization must be in writing or by other means of manifestation of the owner will, and it is stated from paragraph 2 [2] that in case the authorization is in writing it must be highlighted in the contractual clauses. in the case of processing sensitive personal data, article 11, clauses 1 [2] , states that with the consent of the holder, and article 14, paragraph 1 [2] , which states must have the consent of parents or legal guardians concerning the processing of personal data of children and adolescents. in gdpr [10] it is also explicit that for any activities that require a data processing must have the consent of the data holder, in article 6, paragraph 1, clauses a [10] , it says that data processing will be lawful upon the consent of the data holder for specified purposes previously informed to the data holder, in article 7 [10] which sets out the conditions applicable to consent, it says that the data processing agent must prove that the data holder has agreed to the specified purposes. as regards the processing of data on children, article 8 of the european regulation [10] requires the person legally responsible for the child under the age 16 to consent to the processing. the state may be responsible for giving consent if the child is under the age of 13 and has no family members to answer for him or her. without a reference law for the use of personal data, the possibility of abuse in the collection and use of personal data is increased, as well as the encouragement of several other non-specialized bodies to issue their opinions regarding the use of data, which causes great confusion. this is the case, for example, of inspections and inspections by the public prosecutor's office and consumer protection agencies, the issuance of opinions by regulatory agencies, or even judicial decisions based on various sparse legal provisions [1] [5] that seek to define parameters for the processing of personal data. in the graph (figure 3), shows the level of interest in internet users searches on the terms lgpd and gdpr over a twelve-month period, where the term lgpd represents the blue line and the term gdpr represents the red line, on the horizontal axis represents the time and on the vertical axis represents the level of search made on the terms, these levels are represented by the numbers 0 (very low), 25 (low), 50 (average), 75 (high) and 100 (very high). this simple analysis shows that the red line had several peaks in some periods, this because the gdpr since 2016 [10] is approved and had an adequacy period of two years and the level of interest is between average and very high, the blue line has had small peaks, this because the lgpd is a new subject in brazil and this makes the level of interest is between very low and average. in general, users looking for lgpd and gdpr terms are professionals in the juridical environment or information technology. it should be noted that both the brazilian law and the european regulation, they provide a guide for data processing and what procedures companies should take to comply with the law if these principles are not followed these companies will be at serious legal risk. an example of noncompliance with the law was the cambridge analytica scandal [15] , which misused data from 87 million facebook users (figure 4), manipulated the data without the consent of the data holders, to help win donald trump's us presidential campaign, and for the british to vote to leave the european union, both in 2016 [15] , facebook was asked about data security. in brazil, there have been several cases of data loss, such as the case of the netshoes website, according to the coordinator of the commission for personal data protection, prosecutor frederico meinberg, "this is one of the largest security incidents recorded in brazil" [17] , which because of the data leak could put the integrity of 1,999,704 users at risk if the leaked data fell into the wrong hands. the impact that data leaks go far beyond the financial losses, the exposure of each citizens' information can be irreversible damage that becomes impossible to measure the size of the loss. without an information security policy, it can cause serious problems such as the invasion of vital systems to steal tax returns, data, making illegal financial transfers, interrupting the strategic operations of a company, or the government. another case about data leakage was written by liliane nakagawa and published on the website olhar digital [18] , which displays the news about the banking institution, specifically the bank of brazil provident fund [17] . according to nakagawa, data leak that reaches 153 thousand clients -official number of registered in the bb previdencia platform, according to bank of brazil. the source, who identified the security gap, stated that through the private pension system, aimed at companies and public agencies, it is possible to have access to all personal data of participants and, from breaking, editing and registering beneficiaries, all in the name of the registered person himself [18] . after this news, several headlines were reporting the incident, the exame magazine published on its website, "bb previdencia website leak exposes data of 153 thousand clients" [19] , the newspaper, o estado de s. paulo, published on its website, "security sheet on bb previdencia website exposes client data" [20] (figure 5). for these leaks not to occur, companies must have a data protection officer -dpo [2] [10], where the primary function is to ensure that the organization processes the personal data of their employees, their customers, their suppliers or any other individuals securely and reliably according to the data protection rules of law [10] . an lgpd will give the right to protection of the personal data of the respective holders and will give guidelines to the companies on how the treatment should be done. brazil will be adapting to gpdr and will move the job market for data protection specialists. however, brazil [21] already has a law for the creation of a supervisory body to verify whether companies comply with the lgpd, but directors have not yet been appointed to the national data protection authority -anpd and the national council for personal data protection and privacy [8] . the european body responsible for supervising undertakings on whether they comply with the european regulation is the european data protection supervisor -edps, an independent supervisory authority established according to eu regulation 2018/1725, and its task is to ensure that the fundamental rights and freedoms of individuals -in particular their privacy -are respected when eu institutions and bodies process personal data. in the world, there are already some countries [22] outside the eu that have a regulation regarding data protection. on the european commission's website, it informs countries that are at an appropriate level to the regulation, the european commission has recognized andorra, argentina [23] , canada (trade organizations), faeroe islands, guernsey, israel, isle of man, jersey, new zealand, switzerland, uruguay [23] and the united states of america (limited to the privacy shield framework) as providing adequate protection [24] . through the internet civil framework, which establishes rights and duties, guarantees and principles for the use of the internet in brazil, it does not guarantee data protection and privacy in a well-structured, complete and comprehensive manner, nor is a general regulation on the protection of personal data, and its provisions on data protection not protective in nature. some of the challenges identified for implementing the law in brazil are legal adjustments and appropriate training, a complete action plan for companies to comply with lgpd, specialized implementation of personal data governance processes, information security technologies, educating brazilian society about this law by showing the rights and duties of citizens. therefore, there will still be a lot of debates and discussions about lgpd and whether it will adhere to gdpr, and how brazil will behave with the law when it becomes effective. estabelece princã­pios, garantias, direitos e deveres para o uso da internet no brasil, marco civil da internet dispãµe sobre a proteã§ã£o de dados pessoais e altera a lei nâº 12.965, de 23 de abril de 2014 (marco civil da internet) lei nâº 9.296, de 24 de julho de 1996. regulamenta o inciso xii, parte final, do art. 5â° da constituiã§ã£o federal dispãµe sobre a proteã§ã£o do consumidor e dã¡ outras providãªncias. diã¡rio oficial da uniã£o, 12 de setembro de medida provisã³ria nâº 959, de 29 de abril de 2020. regras para o auxã­lio emergencial e adiamento da vigãªncia da lgpd vacatio legis -senado notã­cias altera a lei nâº 13.709, de 14 de agosto de 2018. para dispor sobre a proteã§ã£o de dados pessoais e para criar a autoridade nacional de proteã§ã£o de dados; e dã¡ outras providãªncias. diã¡rio oficial da uniã£o dispãµe sobre a proteã§ã£o de dados pessoais e altera a lei nâº 12.965, 23 de abril de ue) 2016/679 do parlamento europeu e do conselho, de 27 de abril de 2016, relativo ã  proteã§ã£o das pessoas singulares no que diz respeito ao tratamento de dados pessoais e ã  livre circulaã§ã£o desses dados e que revoga a diretiva 95/46/ce (regulamento geral sobre a proteã§ã£o de dados) directiva 95/46/ce do parlamento europeu e do conselho de 24 de outubro de 1995 relativa ã  proteã§ã£o das pessoas singulares no que diz respeito ao tratamento de dados pessoais e ã  livre circulaã§ã£o desse dado. luxemburgo unlocking the eu general data protection regulation setor de tecnologias educacionais -seted cambridge analytica teve acesso ã  87 milhãµes de contas an update on our plans to restrict data access on facebook netshoes deverã¡ procurar 2 milhãµes de clientes afetados por vazamento, diz mp previdãªncia privada do banco do brasil vaza dados de 153 mil clientes vazamento de site da bb previdãªncia expãµe dados de 153 mil clientes falha de seguranã§a em site da bb previdãªncia expãµe dados de clientes -economia -estadã£o quais os princã­pios do gdpr e seu impacto no brasil? proteã§ã£o de dados na amã©rica latina european commission -european commission google trends -c trends tools has experience in computer science, with emphasis on information systems, working mainly on the following topics: artificial intelligence, paraconsistent analysis network, paraconsistent logic, industry 4.0, and artificial neurons brazil. i also received the doctor degree and livre-docente title from the same university. he is currently the coordinator of the logic area of institute of advanced studies -university of sao paulo brazil and full professor at paulista university -brazil. his research interest topics include paraconsistent annotated logics and ai, ann in biomedicine, and automation, among others. he is a senior member of ieee master's degree in production engineering in the area of artificial intelligence applied to software paraconsistent measurement software, post-undergraduate degree in ead, university professor, general coordinator of it course and campus assistant it consultant and/or roles: it director, commercial director, project manager, with clients: wci-mahlerti has experience in science and technology, with emphasis on information technology post-graduate -teaching for higher education falc -faculty aldeia de carapicuã­ba post-graduate -specialization in business intelligence faculty impacta de tecnologia -fit, itil expert certification; iso 20000 certification; privacy data certification; dpo privacy and data protection foundation certification this study was financed in part by the coordenaã§ã£o de aperfeiã§oamento de pessoal de nã­vel superior -brasil (capes) -finance code 001. key: cord-261311-j6bmgmhz authors: parreiras martins, maria auxiliadora; fonseca de medeiros, amanda; dias carneiro de almeida, claudmeire; moreira reis, adriano max title: preparedness of pharmacists to respond to the emergency of the covid-19 pandemic in brazil: a comprehensive overview date: 2020-07-31 journal: drugs ther perspect doi: 10.1007/s40267-020-00761-7 sha: doc_id: 261311 cord_uid: j6bmgmhz the outbreak of covid-19 in lowand middle-income countries is worrisome due to the social inequalities in these countries, their limited health budgets and the significant burden of other acute and chronic diseases. the leap in the number of cases in brazil has imposed a huge strain on the healthcare system. we sought to provide a comprehensive overview of the challenges encountered by pharmacy services in responding to the covid-19 pandemic emergency in brazil and discuss the role of clinical pharmacists in this context. pharmaceutical services play a key role in the emergency response to the pandemic. the pharmacy workforce has been actively working to manage drug shortages, redesign workflow, and review drug formularies/protocols to improve safety for patients and healthcare professionals (hcps). covid-19 patients may present high risk in the use of medications and clinical pharmacists can contribute substantially as part of a multidisciplinary team to improve outcomes in drug therapy in severe and critical illness. the participation of pharmacists as members of antimicrobial stewardship programs should be enhanced to ensure appropriate and safe use of antibiotics in this context. hcps should be encouraged to seek improvements in the performance of pharmaceutical services and innovative practices to respond to the pandemic. further studies are needed to generate knowledge on covid-19 to improve patient care in vulnerable populations. coronavirus disease 2019 (covid19) is an emerging infectious disease first described in wuhan, china, in december 2019, caused by the novel severe acute respiratory syndrome coronavirus (sars-cov-2) [1] . the outbreak of covid-19 spread rapidly worldwide, being declared a pandemic on 11 mar 2020 by the world health organization (who). human-to-human transmission occurs via droplets or contaminated hands or surfaces [1] . various levels of classic public health strategies, such as social distancing, isolation, quarantine, and community containment, have been applied across countries to reduce the dissemination of the disease [2] . by july 2020, sars-cov-2 had infected >14 million people in 216 countries, creating an enormous burden on healthcare systems and the economy [3] . it reached the southern hemisphere later than the other continents and the progress of its transmission in the winter 'flu' season is unclear. the infection spread in low-and middle-income countries (lmics) is worrisome due to their inability to respond rapidly to a pandemic situation in a scenario of social inequalities, limited health budgets, and the significant burden of other acute and chronic diseases [4, 5] . the clinical spectrum of covid-19 is heterogeneous, encompassing asymptomatic disease, mild upper respiratory tract infection, and severe viral pneumonia that may progress to critical illness and death [6, 7] . common signs of the disease include fever, myalgia, cough, and dyspnea [8] . around 20% of confirmed covid-19 cases develop severe or critical illness [6] , representing the subgroup of patients who are challenging frontline healthcare professionals (hcps) in hospitals. prognosis is poor for older adults [9] and in the presence of comorbidities, such as cardiovascular diseases [8, 10] . knowledge regarding covid-19 is being acquired at the bedside during the accelerated race to find efficacious drug treatments and vaccines. worldwide, clinical trials have been designed to investigate the efficacy and safety of old and new drug candidates as treatments for covid-19, but no guidelines have been established thus far [11] . in the context of assistance to covid-19 patients, pharmacy services need to consider adjustments in drug supply, workflow, and pharmaceutical care. we sought to provide a comprehensive overview of the challenges encountered by pharmacy services to respond to the covid-19 pandemic emergency and to describe its role in the brazilian context. the first case of covid-19 in brazil was officially confirmed on 25 feb 2020, and the infection has spread rapidly, infecting 2,012,151 individuals by 18 july 2020, with 76,688 deaths [3] . brazil is in second place with regard to the number of cases and deaths, being declared by the who as the new epicenter of the coronavirus outbreak. due to the low testing capacity, testing of severe cases has been prioritized and the total number of cases is still underestimated. according to the brazilian ministry of health, the number of hospitalizations to manage acute respiratory distress syndrome (ards) was >600% higher in 2020 than the same period in 2019 [12, 13] . the transmission of the virus is not yet controlled and brazil has been reported to have the highest rate of transmission (r0 of 2.81) among 48 analyzed countries [14] . it is hypothesized that covid-19 was imported by wealthy brazilians who travelled abroad and then transmitted locally to poor communities, who mostly live in precarious conditions [15, 16] . social isolation and containment measures, as well as hygiene recommendations, are almost impossible to follow in these environments. healthcare in brazil is provided by public and private health systems. the first suspected and confirmed cases of covid-19 were referred to private services, but later poor people began to seek assistance in the public system. brazil is a large south american country with 26 states with diverse social, cultural, and economic backgrounds. hospital beds are unequally distributed across the country and most beds in intensive care units (icus) are concentrated in the southeast region. people requiring ventilation support may outnumber the available ventilators and icu beds [5] . in this context, covid-19 remains unequally spread in a country with a political scenario of uncertainties [17] , involving instability in the ministry of health and polarization in the political and ideological fields. to provide assistance of quality in the middle of a crisis is extremely challenging, especially if we consider the particularities of our population. prior to the emergence of covid-19, brazil had undergone a transition in epidemiological age, related to decreasing mortality and increasing life expectancy [18] , with a projected increase in the population aged >60 years of almost threefold by 2050 [19] . the burden of chronic conditions, including diabetes mellitus, cardiovascular diseases (e.g., ischemic heart disease and stroke), cancer, and obesity is growing. additionally, the public healthcare system still needs to cope with chronic infectious diseases, including hiv/aids, tuberculosis, syphilis, and malaria, and also endemic and emerging vector-borne arboviruses, such as yellow fever, dengue, zika, and chikungunya [18] . in late march 2020, scheduled elective healthcare procedures and appointments started being gradually cancelled within brazilian states to prevent virus transmission. strategies have been implemented to reorganize the available beds to assist covid-19 patients and other emergency clinical and surgical patients, and increase the number of beds by building temporary field hospitals where necessary. healthcare settings have restructured workflow, adapting protocols to address new requirements of biosafety and providing training to staff. despite the lack of conclusive scientific evidence, protocols are being rapidly updated to improve safety for patients and hcps. pharmaceutical services have been encouraged to be actively involved in various steps of these processes. the early experience of pharmaceutical services during the outbreak of covid-19 in china highlighted the indispensable work of community [20, 21] and hospital [22] pharmacists in the emergency response to the pandemic [23] . the international pharmaceutical federation (fip) released the "coronavirus 2019-ncov outbreak: information and interim guidelines for pharmacists and the pharmacy workforce", drafted with the participation of the chinese pharmaceutical association (cpa), to provide reliable information on the management of pharmacy operations [24] . the pharmacy emergency preparedness and response (pepr) recommendations were published to guide pharmacy endeavors towards full integration within public health and in recognition of pharmacists' skills, roles, and contributions as integral members of multidisciplinary healthcare teams [25] . these references can be used to create regional guidance for pharmacists and adapted to local demands and resources. the brazilian society of hospital pharmacy released recommendations for pharmacists working in different scenarios to fight against the pandemic [26] . an economic disruption without precedent has occurred together with a dramatic increase in the consumption of health products worldwide. global drug shortages were triggered by inadequate quantities of raw materials, procurement and manufacturing issues, and drug discontinuations [27] . in brazil, drug shortages also involved importation difficulties, exorbitant costs, compulsory advance payments, and noncompliance with agreed quantities and delivery deadlines. the supply of essential drugs has been jeopardized, including sedatives (fentanyl and midazolam) and neuromuscular agents (suxamethonium, atracurium). commitment of pharmacists is required to manage drug shortages and minimize the impact on patient outcomes [23, 25, 27, 28] . the brazilian population has been impacted by a flurry of fake news. the fear of catching covid-19 and free access to drugstores have caused a rush to buy medicines for selftreatment. data presented by the federal board of pharmacy revealed a substantial increase in drug sales involving ascorbic acid (180.0%), acetaminophen (77.4%) and hydroxychloroquine sulfate (67.9%) from january to march 2020 relative to the same period in 2019 [29] . the off-label use of chloroquine/hydroxychloroquine for preventing or treating covid-19 imposes safety issues and requires the implementation of prescription monitoring strategies [30] . panic buying of alcohol-based formulations, face shields, n95 respirators and other personal protective equipment (ppe) has also occurred, leading to shortages in hospitals and other healthcare facilities. the supply has been partially restored after government interventions and the recommendation to the public to wear fabric face masks. population health interventions and the support of pharmacists for the rational use of drugs was shown to be of utter importance in this scenario. the brazilian branch of the institute for safe medication practices (ismp-brasil; https ://www.ismp-brasi l.org/ site/) has provided important contributions for this approach. another concern is the effect of covid-19 on increasing morbimortality of patients with chronic diseases, given their compromised access to healthcare and diagnostic tests. delays in assessment may worsen the prognosis of chronic diseases. kretchy et al. [31] discussed the challenges of managing chronic diseases and promoting medication adherence in lmics. community pharmacists were identified as front-line personnel to promote healthy lifestyle adjustments, refill prescriptions, provide counseling on the management of chronic diseases, and minimize unsafe self-medication habits with over-the-counter medicines. pharmacists working through telehealth services could enhance outcomes in drug therapy and mitigate strategies to reduce the risks of covid-19 contagion, such as triaging people with flu-like symptoms and improving workflow for physical distancing and self-protection [25, 32, 33] . strategies to support the public and hcps to cope with stress, anxiety, and poor sleep quality during the pandemic have been reported worldwide [25, 33, 34] , and remote services have gradually started to operate with this aim in brazil. however, the number of people with access to remote assistance is still limited. pharmaceutical services have been adjusting to respond to the covid-19 outbreak at the level of public and private institutions, with attempts to meet the needs of patient care in each brazilian region, according to the available financial and human resources. hcps and students have been recruited by the ministry of health through the program "brasil conta comigo" ('brazil counts on me') as volunteers to face the pandemic. basheti et al. [35] investigated the pharmacists' and pharmacy students' awareness of their role during this emergent situation in jordan and the source of their information on covid-19. in brazil, the education and training of pharmacy professionals and students are under intense discussion in universities and healthcare settings. live broadcasts, remote trainings and recorded courses using the internet and other media are being used as important means of education. pharmacists have been working on laboratory testing for covid-19, administration of pharmacy supplies and replenishment, and also patient care, replicating experiences in other countries [20, 23, 33, 36] . attributes of pharmaceutical services in the community and hospital settings in brazil are summarized in fig. 1 . in community pharmacies, actions are focused on patients, comprising provision of information on covid-19, promotion of the safe use of medicines, and guidance on medication adherence in acute and chronic diseases. in hospital pharmacies, beyond interactions with patients, pharmacists develop integrated actions with multidisciplinary teams in different fields of expertise, such as emergency and intensive care. hospital pharmacists, in partnership with infection control committees, have produced remarkable results in the internal review of work processes, including rotation of working hours, home offices, distancing between workers, intensification of environmental control measures and self-protection of workers, new guidance on the use of sanitizers, and training on good practices for self-care at home, on the move, and at work. hospital pharmacies seek to optimize clinical, humanistic, and economical outcomes in drug therapy by performing medical history and drug therapy reviews, patient follow-up, and medication reconciliation to ensure safe transition of care, as well as participating in antimicrobial stewardship programs (asps). pharmacists in community and hospital settings should enhance medication safety strategies and precautions in special populations with the aim of reducing avoidable harm related to medications. the development and refinement of pharmacists' role in the community and hospital settings is heterogeneous across regions. however, establishing robust organization of pharmacy services with clear planning of structure, processes, and outcomes' assessment [25] could contribute to ensuring the quality of the response to the pandemic. reimbursement issues need to be addressed and advanced in brazil. the pharmacy workforce need to understand the nature of covid-19, how it is transmitted, and how to prevent its spread [24] . clinical pharmacists should constantly seek updated knowledge on covid-19 to improve the monitoring of effectiveness and safety of drug therapy, and to promote productive interaction within the multidisciplinary team [25] . however, at the time of writing, high-quality evidence to support pharmacologic treatments for covid-19 is still lacking [37] . whilst waiting the results of ongoing clinical trials, experimental treatments are being used worldwide. various protocols have been proposed by different committees and institutions in brazil. on 18 may, a consensus of the brazilian association of intensive medicine, brazilian society of infectology and brazilian society of pneumology and tisiology was published as a reference for the pharmacological treatment of covid-19 [38] . off-label drugs currently used in brazil include hydroxychloroquine (chloroquine) solely or in combination with azithromycin, lopinavir/ritonavir/oseltamivir, tocilizumab, glucocorticoids and parenteral anticoagulation. due to conflicting scientific evidence, hcps should reach a consensus, with decisions on drug therapy being individualized, based on disease stage, risk/benefit assessment, and pharmacoeconomic aspects. pharmacovigilance is needed to monitor the safety of experimental treatments and provide up-to-date guidance to hcps. for instance, increasing numbers of patients with ards are receiving empirical treatment with oseltamivir due to limitations of covid-19 testing, which may increase the risk of drug toxicity. in brazil, the national health surveillance agency (agãªncia nacional de vigilã¢ncia sanitã¡ria; anvisa) is responsible for evaluating adverse drugs events (ade) notifications made through the vigimed â® system. clinical pharmacists play a key role in the identification and reporting of these ade, especially in the critically ill. individuals with severe or critical covid-19 should be considered high-risk patients with regard to the use of potentially beneficial therapies and should be closely monitored by clinical pharmacists. liver and kidney injuries in covid-19 may alter the pharmacokinetics of drugs currently prescribed to treat the disease. lopinavir/ritonavir/ oseltamivir, hydroxychloroquine and chloroquine are metabolized in the liver and most of their metabolites depend on renal excretion. therefore, injury to the liver and kidneys can hinder metabolism, excretion, and the achievement of desirable serum concentrations, increasing the risk of drug toxicity [39] . pre-existent liver and kidney diseases, impairment of these organs in older adults, and the presence of comorbidities can elevate the risk of clinical complications in covid-19 [10, [39] [40] [41] . other parameters to monitor effectiveness and safety of drug therapy should be included in clinical pharmacy protocols. thromboprophylaxis in covid-19 using non-fractionated heparin or low-molecular-weight heparins has been used to control the hypercoagulability state in hospitalized patients [42, 43] , with multiple pharmacological mechanisms previously described [44, 45] . risk-benefit assessments of anticoagulation therapy should consider individual contraindications, stratification of bleeding risk, and dosage adjustments in patients with renal impairment and obesity [46] . the use of proarrhythmic medications should also be closely monitored. patients receiving hydroxychloroquine or chloroquine â± azithromycin should be frequently monitored for cardiac toxicity by checking their corrected qt (qtc) interval and for the use of other medications with a risk of qtc interval prolongation or torsade de pointes [47] . additionally, the empiric use of antibiotics for suspected secondary bacterial infections needs to be optimized on initiation and rigorously de-escalated [48, 49] . hospitals should not lose sight of the long-term threat of antimicrobial resistance, if their current structures and asps are disrupted during the pandemic [50] . hence, the participation of clinical pharmacists with advanced infection disease training as members of asps is fundamental in ensuring appropriate and safe use of antibiotics and improvements in the quality of care. however, the involvement of asps in the covid-19 response is still incipient despite being recommended by experts in this field [51] . the use of medications should take into account special populations, including pregnant [52] , pediatric [53] , breastfeeding [54] , and cancer patients [55] . the desirable attributes of clinical pharmacists to provide care for hospitalized covid-19 patients in brazil are summarized in table 1 . due to the lack of definitive protocols, the management of covid-19 has been primarily supportive [49] . the fasthug-maidens mnemonic (table 1) is a standardized structured approach for pharmacists to identify drug-related problems in icus [56] . several authors have described potential markers of critical illness, staging, or disease recovery in covid-19 (e.g., d-dimer, lactate dehydrogenase, interleukin-6) [8, 10, 43, [57] [58] [59] [60] . the course of an intense inflammatory process leads to alterations in many review of patients' medical history provision of real-time assessment and evidence-based (when possible) advice on drug therapy support on safe use of medications brought from home medication reconciliation at different levels of transition of care simplification of drug administration schedule to reduce the exposure of nurses to covid-19 patients monitoring of potential drug-drug, drug-food interactions and adverse drug reactions adjustments in dosing regimens according to liver and kidney functions prevention of medication errors optimization of drug therapy and electrolytes to minimize the risk of prolonged corrected qt intervals and torsade de pointes support on lung-protective ventilation and neuromuscular blocking agents to facilitate ventilator synchrony provision of conservative fluid strategies and monitoring of vasopressors use monitoring of empirical antibiotics for suspected bacterial co-infection with rigorous de-escalation employment of fasthug-maidens mnemonic to identify drug-related problems in intensive care units support on drug information to patients and multidisciplinary teams, following biosafety protocols considerations on special situations (pediatrics, older adults, people with chronic diseases, allergies) research and continuing education precise documentation of pharmaceutical interventions laboratory tests in patients with acute or severe/critical illness. specific guidance on the use of laboratory tests to predict critical illness in covid-19 is under investigation [61] . thus, to date, laboratory tests need critical interpretation and hcps should make consensual decisions based on patients' clinical condition. laboratory tests with potential utility to monitor covid-19 in hospitals are listed in table 2 . in brazil, the use of these tests is heterogeneous in healthcare settings, and may be limited due to cost issues, delayed release of results, and the lack of equipment or partnerships between institutions. there are many unanswered questions regarding covid-19. thrombotic risk varies according to race and ethnicity [62] ; however, the impact of the heterogeneous ancestral contributions from african, caucasian, and indigenous genomes in the brazilian populations [5] are not yet clear. regarding the use of medications, the protective effect of chronic use of oral anticoagulants and the clinical impact of ace inhibitors and arbs commonly prescribed to treat hypertension on the risks of covid-19 are currently unclear [40, 49] . furthermore, the association between the complications of severe covid-19 and chagas disease and rheumatic heart diseases, conditions that are still prevalent in brazil [63] , is not established. we also do not know if the determinants of severity in brazil will be similar to those observed in the usa [61] , china, and europe [58, 60] , given other factors such as social inequality and endemic diseases. future studies in brazil should investigate clinical presentation, according to the features of inflammatory response, treatment outcomes, and the factors associated with critical illness. â�¢ pharmacists play a key role in the management of covid-19 in brazil by providing health interventions and specialized support to improve outcomes, especially in populations with underlying diseases and social inequalities. â�¢ pharmaceutical expertise has been relevant in managing drug shortages, redesigning workflow, and educating pharmacists in brazil. â�¢ pharmacists can contribute to multidisciplinary teams, including antimicrobial stewardship programs, to improve outcomes of drug therapy in severe and critically ill patients. â�¢ further studies are needed to improve covid-19 knowledge and patient care in low-and middle-income countries. world health organization. novel coronavirus-china. geneva: world health organization isolation, quarantine, social distancing and community containment: pivotal role for old-style public health measures in the novel coronavirus (2019-ncov) outbreak world health organization. coronavirus disease (covid-19) managing covid-19 in lowand middle-income countries covid-19 in brazil the epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (covid-19) presumed asymptomatic carrier transmission of covid-19 clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study estimates of the severity of coronavirus disease 2019: a model-based analysis clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study race to find covid-19 treatments accelerates ministry of health of brazil, health surveillance department [ministã©rio da saãºde do brasil, secretaria de vigilã¢ncia sanitã¡ria deep impact of covid-19 in the healthcare of latin america: the case of brazil coronavirus contagion rate in brazil is 2.8, the highest among 48 countries, points out imperial college routes for covid-19 importation in brazil covid-19 is deadlier for black brazilians, a legacy of structural racism that dates back to slavery so what burden of disease in brazil, 1990-2016: a systematic subnational analysis for the global burden of disease study united nations department of economic and social affairs recommendations and guidance for providing pharmaceutical care services during covid-19 pandemic: a china perspective community pharmacist in public health emergencies: quick to action against the coronavirus 2019-ncov outbreak hospital pharmacists' pharmaceutical care for hospitalized patients with covid-19: recommendations and guidance from clinical experience coronavirus sars-cov-2/covid-19 pandemic: information and interim guidelines for pharmacists and the pharmacy workforce pharmacy emergency preparedness and response (pepr): a proposed framework for expanding pharmacy professionals' roles and contributions to emergency preparedness and response during the covid-19 pandemic and beyond contingency plan in various pharmaceutical scenarios of the covid-19 pandemic global drug shortages due to covid-19: impact on patient care and mitigation strategies drug shortage: a public health problem federal board of pharmacy -brazil [conselho federal de farmã¡cia-brasil] survey shows how covid-19's fear impacted medicine sales chloroquine and hydroxychloroquine for the prevention or treatment of novel coronavirus disease (covid-19) in africa: caution for inappropriate off-label use in healthcare settings medication management and adherence during the covid-19 pandemic: perspectives and experiences from low-and middle-income countries necessity of pharmacistdriven non-prescription telehealth consult services in the era of covid-19 fighting against covid-19: innovative strategies for clinical pharmacists clinical characteristics and drug therapies in patients with the common-type coronavirus disease 2019 in hunan, china pharmacists' readiness to deal with the coronavirus pandemic: assessing awareness and perception of roles providing pharmacy services at cabin hospitals at the coronavirus epicenter in china pharmacologic treatments for coronavirus disease 2019 (covid-19): a review guidelines for the pharmacological treatment of covid-19. the task force/consensus guideline of the brazilian association of intensive care, the brazilian society of infectious diseases and the brazilian society of pulmonology and tisiology. rev bras ter intensiva liver and kidney injuries in covid-19 and their effects on drug therapy; a letter to editor covid-19 and older adults: what we know new understanding of the damage of sars-cov-2 infection outside the respiratory system anticoagulant treatment is associated with decreased mortality in severe coronavirus disease 2019 patients with coagulopathy a proposal for staging covid-19 coagulopathy heparin: effects upon the glycocalyx and endothelial cells the versatile heparin in covid-19 stratifying therapeutic enoxaparin dose in morbidly obese patients by bmi class: a retrospective cohort study guidance on minimizing risk of drug-induced ventricular arrhythmia during treatment of covid-19: a statement from the canadian heart rhythm society antibiotic use in the intensive care unit: optimization and de-escalation covid-19: the uninvited guest in the intensive care unit (icu) implications for pharmacotherapy covid-19 and the potential long-term impact on antimicrobial resistance involving antimicrobial stewardship programs in covid-19 response efforts: all hands on deck coronavirus disease 2019 (covid-19) and pregnancy: what obstetricians need to know hyperinflammatory shock in children during covid-19 pandemic breastfeeding and respiratory antivirals: coronavirus and influenza covid-19 and cancer: a comprehensive review a standardized, structured approach to identifying drug-related problems in the intensive care unit: fasthug-maidens abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia prediction models for diagnosis and prognosis of covid-19 infection: systematic review and critical appraisal the laboratory tests and host immunity of covid-19 patients with different severity of illness development and validation of a clinical risk score to predict the occurrence of critical illness in hospitalized patients with covid-19 factors associated with hospital admission and critical illness among 5279 people with coronavirus disease covid19 coagulopathy in caucasian patients atrial fibrillation: prevalence in a large database of primary care patients in brazil acknowledgements this study was partially supported by the univerkey: cord-176540-48mapwlq authors: schulz, rodrigo a.; coimbra-ara'ujo, carlos h.; costiche, samuel w. s. title: covid-19: a model for studying the evolution of contamination in brazil date: 2020-03-31 journal: nan doi: nan sha: doc_id: 176540 cord_uid: 48mapwlq in the present article we introduce an epidemiological model for the investigation of the spread of epidemics caused by viruses. the model is applied specifically to covid-19, the disease caused by the sars-cov-2 virus (aka"novel coronavirus"). the sir (susceptible infectious recovered) model is used as a basis for studying the evolution of the epidemic. nevertheless, we have modified some of the model hypotheses in order to obtain an estimate of the contamination free of overestimated predictions. this extended model is then applied to the case of the recent advance of the epidemic in brazil. in this regard, it is possible to obtain the evolution for the number of infectious significantly close to that provided by current data. accordingly, we evaluate possible future scenarios for the disease spread. regarding the population susceptibility, we consider different social behaviors in response to quarantine measures and precautions to avoid contagion. we conclude that the future scenario of the epidemic depends significantly on the social behavior adopted to date, as well as on the contagion control measures. the extent of such measures would be likely to cause thousands, millions or tens of millions of contaminations in the next few months. the emergence of sars-cov-2 epidemic around the world has motivated a series of studies and projections for the evolution of the disease over the next few months. the fight against the spread of the disease occurs in the world by the use of many research techniques, treatments and the prevention of the contamination [1] . in the latter case, one of the main factors associated with virus prevention is related to restrictions in human social contact in order to prevent the unrestrained contagion [2] . however, the absence of a broad scientific literature on the evolution of the virus, as well as the accelerated growth of contamination in brazil during march 2020, give rise to a series of possible predictions. when such predictions are disclosed by the main information vehicles, it is provided scope for minimalist and maximalistic interpretations of the case. in this aspect, adequate projections based on current data is needed. considering such circumstances, it is natural that epidemiological models arise driven by actual available data related to the evolution of the disease. once created the model, it is possible to predict possible future scenarios from which one can have a better indication of the dimension of such an epidemic in the country and in the world. some of the currently known models used in such procedures are sis, sir and sirs [3] . the first one is used mainly in the study of diseases in which recovery does not prevent the re-contamination of the pacient, usually caused by bacterial agents [4] . the second is used for modeling epidemics involving infectious diseases, such as covid-19, caused by sars-cov-2 [5] . the third one is basically used for the study of infections caused by influenza, since it allows the modeling of a situation where recovered individuals lose their immunity (which sir, for example, does not model) [6] . the present work explores the building of a variation of the sir model in order to cover relevant conditions present in the brazilian context, such as: 1) daily mortality and daily birth rates (which change, over time, the population) and 2) the gradual reduction of the population susceptible to the disease in fuction of social distancing measures. here it will be considered a modification in the hypothesis that, initially, the entire population analyzed is susceptible to contamination by the disease. the brazilian situation until march 22 had more than 1,500 confirmed cases of infection, with 25 cases of death from the disease [7] . the exponential growth of infection cases reveals the need to develop studies related to the behavior of epidemics in order to stabilize the current scenario, as well as to allow the advance in the development of tools that permit analyzing the behavior of epidemics in the future from the first cases. other relevant impact of such studies is that they provide concrete justifications for the effectiveness and awareness related to social distancing policies. the paper is divided in sections. the second section reviews the original formulation of the sir model. the third section presents the methodology and the forth section deals with the use of such a methodology in the brazilian case. the fifth and the final sections present some discussion, concluding remarks and prospects. the sir model is based in a simple hypothesis: the individual of a given population where an epidemic occurs goes through different stages of susceptibility to infection [3] . such stages give rise to well defined compartments in the model, where the individual is classified as: from this hypothesis, an epidemic can be characterized as a flow: where the infectious i and recovered r population grow over time, while the susceptible s subject decreases over time. in this way, this flow can be described by functions s(t), i(t) and r(t) such that the evolution of i(t) over time characterizes the number of cases of infection at all times throughout the course of the disease. to characterize the temporal evolution of the model, it is necessary to establish how the instantaneous variation of the functions of the model occurs. for example, if α is the rate of change in the number of infectious individuals (the ratio of infectious to a previous time interval), then the number of new infections at each time interval, in a population of n individuals, reduces the susceptible population as follows: on the other hand, if β is the rate of recovery from the epidemic, then the number of recovered individuals will be a fraction of the number of infectious: at last, the number of infected each day should equal the difference between the number of new contaminations in the susceptible population and the number of recovered from the infected population, that is the sir model also considers that the initial value associated with the functions s(t), i(t) and r(t) can be defined assuming that, initially, the entire population is susceptible to infection, that there is a minimum population d, initially infectious (otherwise there would be no way for the epidemic to start), and there is no one recovered, since the epidemic did not started. in other words: in this way, the temporal evolution of the functions described by the sir model consists of an initial value problem involving a system of three ordinary differential equations. in the previous section, the sir model was presented as a proposal for modeling an epidemic. the system of equations is reasonably simple. however, its construction requires some hypotheses whose acceptance may imply an overestimated forecast of the number of people infected by the epidemic. are they: i -initially, the entire population is susceptible to contamination. ii -there are no deaths or births over the course of the epidemic. iii -there are no reductions in the susceptible population, for example, due to quarantine measures. those processes significantly interfere in estimating the number of people infected. in respect to i, for example, why should one suppose that the contamination of one person in são paulo on february 26 would imply that someone in the state of roraima (∼ 4, 500 km away) would be susceptible to contamination on february 26? the susceptibility to contamination is directly related to the proximity between contaminated individuals, but in this case, if both are separated by long distances, without maintaining any contact, then there is no reason to suppose that there is a relationship of susceptibility between them. regarding ii, it is well known that several deaths of people, contaminated or not by the disease, occur throughout its evolution, interfering in the number of susceptible individuals. similarly, the more people born the more susceptible to contamination they become, promoting an increase in the number of cases. and in respect to iii, it is assumed that, with the evolution of the epidemic, people will begin to isolate themselves socially, whether by individual will or governmental determination, so that the susceptible population is also reduced due to this factor [8] . this means that the forecast of the sir model is naturally overestimated to calculate the number of people infected daily on a value of s(t) which can be many times greater than the real one. to correct the problematic points in assertions i, ii and iii, one can add terms in the equations (1), (2) and (3) in order to operate them according to the logic of a growing susceptible population, where there are reductions resulting from deaths and from social isolation processes, as well as an increase in the number of susceptible people due to the birth rate. given a population n , the sir model originally supposes that s(0) = n and s(t) < s(0), ∀t > 0. here, in order to correct the fact pointed out in i, it is supposed that s(0) = (1−ρ 0 )n , where ρ 0 is the percentage of the population initially isolated from contamination, and that ds(t) dt evolves so that the rate ρ 0 decreases over time, i.e. where and ∆ρ is the mean rate of the growing of the susceptible population with the disease evolution. in this respect, the smaller the value of ρ 0 is (a value between 0 and 1) the more the initial population approaches n . besides, the greater ∆ρ is the faster the susceptible population approaches the total population. for example, a reasonable estimate for ρ 0 is to consider the initial susceptible population as the population of the place where the epidemic begins, taking the ∆ρ rate as the mean percentage of the growing of the susceptible population, parameterized by the total time required for the epidemic to reach all the domains of a given country. that is, if ∆t * is the time required for the epidemic to reach all the domains (states) of a country in which the epidemics occurs, then the mean number of new susceptible individuals in each day will be n = n ∆t * , and the percentage of new susceptible people each day will be ∆ρ = n n . in this case, ∆ρ can also be interpreted as the inverse of the period necessary for the epidemic to reach the whole country, because this change also implies that the number i(t) of contaminated individuals will increase at the same rate that s(t) decreases, that is, depending on the gradual increase in the susceptible population: to correct the value of the population susceptible to contamination due to deaths and daily births, just add terms to the equation (4) that relate the mortality rate and the daily birth rate to the susceptible population s(t). that is, if γ is the percentage of the population that dies daily due to something unrelated to the epidemic, and θ is the daily rate of people that born in the place where the epidemic occurs, then the variation in the susceptible population will be proportional to the difference between the number of people who born and the number of people who die, i.e. where p (t) expresses the variation in the number of susceptible people, per day, due to mortality and birth rates. when adding p (t) to the equation (4), we get it may happen that, after some period after the beginning of the evolution of the epidemic, there is a dramatic reduction in the population s(t) due to social distancing measures. the cancellation of classes in public schools and universities, commercial and industrial activities, as well as musical concerts and similar events are examples of how these reductions can occur. thus, it is possible that there is a time τ such that the susceptible population will be reduced with the rate k of its default value. when this occurs, the equation (8) should start to consider the new population as the contingent under which the contamination factor α acts. to characterize this process, it is possible to define the functions s(t) and i(t) by parts, as follows: this process occurs in such a way that the population s(t) tends to increase with time, since ρ(t) decreases with time, but it also tends to decrease with the factor k (from τ ). that is, if the proportion k of people who begin to isolate themselves in quarantine is greater than the rate at which the susceptible population increases (parameterized by ρ(t)), then the epidemic will begin to decrease. on the contrary, if the rate at which people become susceptible is greater than the rate at which they become quarantined, then the epidemic process will continue to grow until it reaches its maximum. it is also possible to generalize this definition by parts so that, for each t 1 , t 2 , t 3 , ..., t n where quarantine processes are started, one can respectively consider the factors k τ , k τ +∆t 1 , k τ +∆t 2 , ..., k τ +∆tn which act by decreasing the susceptible population. therefore, from the nth instant t, the equations ds(t) dt and di(t) dt will be considered under the form: the obtained system of equations, after the proposed modifications, can be summarized as follows: s(0) = n ; 0 < ρ 0 < 1; i(0) = 0; r(0) = 0; α, β, γ, ∆ρ, k τ +∆tn ∈ r. a very simple way to find the solutions to the initial value problem is to obtain an approximation for the derivatives of s(t), i(t) and r(t) from the taylor series and, following the euler method, obtain the values of s(t + ∆t), i(t + ∆t) and r(t + ∆t) as follows: where ∆t is the step of the solution, determined by the upper and lower limits of the interval at which the solution is calculated 1 , as well as the number of subdivisions in the n range, that is: so that the solution is calculated in the interval [t i , t f ]. in view of the reformulation of the sir model, we can consider its application to describe the evolution of the covid-19 epidemic. in brazil, it can be considered that it started on february 26, 2020 [2, 7, 12] . first, it is necessary to characterize the parameters that define the evolution of the epidemic in the country. the brazilian population is among the largest in the world, with around 211, 720, 000 people [9]. thus, for simulating the evolution of the epidemic in brazil, it can be assumed that: n = 211, 720, 000 people. in addition, for the simulation, it is assumed that the mortality rate in the country follows the global annual rate of 7.7/1, 000 people per year [10] . in order to simulate a daily 1 see the appendix evolution, the daily percentage rate corresponding to the number of deaths per year must be considered: γ = 7.7 1, 000 × 1 365 days = 2.11 × 10 −5 day . regarding the birth rate, brazil registered 2,899,851 births in 2018, according to data from ibge (brazilian institute of geography and statistics) [11] . in this way, the mean daily birth rate, defined in terms of the 2018 data, provides a daily birth rate given by θ = 2, 899, 851 211, 720, 000 × 1 365 days ∼ = 3.75 × 10 −5 day . according to information released by the adolfo lutz institute, the first confirmed case of covid-19 in brazil occurred on february 25, 2020, in the case of a patient who was in são paulo [12] . thus, since it is necessary to assume a minimum initial value of contamination to evolve the epidemic, the simulation will occur from february 26th to the current date. therefore, being sure of the first contamination, and the active action of the contaminated person in relation to the spread of the virus, for the simulation, it is assumed that d = 1, t i = 0 → february 26. as the patient was in the state of são paulo, it is reasonable to assume that the population initially susceptible is that of the state itself. thus, it is assumed that ρ 0 (the population initially free from contamination) is the total population, except for the population of the state of são paulo, about 21 % of the brazilian population [13] . so: in addition, until march 21 (24 days after the outbreak of the epidemic), the ministry of health recognized that community transmission of the virus had reached the entire country [14] , so that the period required for susceptible population to reach the entire country is 24 days, and thus, from equation (6): finally, it remains to determine the values of α and β from the current scenario of the epidemic in brazil. according to data obtained by the worldometer [15] platform, brazil had, until march 28, the number of 3,904 confirmed cases of covid-19 distributed in the time series illustrated in figure 1 . [15] . the mean growth rate α is defined as the mean of the ratios of the number of cases on the following day in relation to the previous day. that is, in this case: where n = 1 corresponds to february 26, and n = 25 corresponds to march 22 2 . for the recovery factor β, a similar procedure is performed, considering the mean of the ratio of the number of recovered to the number of contamination cases. due to the unavailability of the data, however, it is assumed that the brazilian recovery factor follows the world average [14] , i.e. finally, it is also assumed that, starting on march 14, there are five factors 3 (k 17 , k 22 , k 23 , k 26 , and k 28 ) that make it to be reduced by 20 %, 5 %, 5 %, 10 %, and more 5 % on march 14, march 19, march 20, march 23, and march 25, respectively . these values are arbitrary due to the lack of concrete data about how many people are in fact isolated from contamination by quarantine, and express the trend, from these dates, of the reduction of contamination determined by the variations in the the curve illustrated in figure 1 . considering these data, the result of the simulation between february 26 and march 28 is illustrated in figure 2 . given the satisfactory adjustment close to the curve of real data, one can consider the extent of the simulation results for the future. however, as there is currently no specific scenario regarding the factors of reduction of the susceptible population due to social distancing measures, several possibilities can be explored. the first of these is not to consider, from april onwards, that social isolation measures are taken, that is, to remove the k 31 factor from the 34th day of the disease evolution (corresponding to the 31st of march). two other possible cases can be explored by imposing conditions of future social distancing, in order to verify the effect of such measures. figure 4 shows the evolution of the epidemic for the first case, where there are no restrictive measures in the future, and two other cases where the population promotes social isolation keeping it at 50 % until the end of the epidemic and, lastly, raising the percentage of the quarantined population by 20 % from april 10, that is, the comparison between the absence of social isolation measures, and measures reaching 50 % and 70 % of the population, respectively in the first case, a worrying scenario occurs, where the peak of contamination reaches practically 39 % of the population on april 13. in the second case, the 50 % reduction in the susceptibility of the population results in a peak of contamination that reaches around 18.3 % of the brazilian population on may 5, which consists of a considerable reduction in relation to the first case. in the latter case, with isolation conditions reaching 70 % of the population, this peak of cases reaches about 3 % of the brazilian population, on june 29. these results show how social distancing measures alter the dynamics of the epidemic in the country in order to decrease the peak and the total number of cases, as well as to extend the time necessary for the epidemic to reach a maximum in the number of contaminations. additionally, these results may raise the following question: given an instant τ , how restrictive should social isolation measures be? that is, what is the best estimate for the value of k τ ? in section 3.1.3 we showed how it is possible to consider population reduction rates as a result of social isolation measures. so that, for the instant τ , it follows one way to estimate the value of k τ in this case is to make the number of new contaminated individuals null, i.e. this condition does not guarantee that new contamination will cease to occur completely, since it would be necessary to keep the entire infected population in isolation, which is not taken into account by the model, and may often not be a measurable data from the country's statistics. in theory, if all people infected by the epidemic are known, then it would not be necessary that the social isolation condition to extend to the susceptible population. however, in cases where an emerging epidemic begins to evolve and the actual number of infected people is not known, the equation (9) is the best estimate for how restrictive measures of social isolation should be. in the case of brazil, taking march 25 (28 days after the epidemic started), march 31 (34 days after the epidemic started) and april 10 (44 days after the epidemic started) as a reference, we obtain respectively the values: thus, it is possible to note that the longer the time at which social isolation measures are implemented, the more restrictive they must be in relation to the number of people quarantined. thus, given a very long period of time, the value of k τ will require that the entire population establish measures of social isolation, since because ∆ρ is always greater than zero. these three possible future scenarios are consistent with the actual situation of the epidemic in brazil. that is, with respect to the actual data available to date, the three scenarios are possible and depend exclusively on how future actions related to social behavior will be taken. in this respect, the development of epidemiological models capable of predicting the evolution of the epidemic in the face of social behavior is an important tool for raising awareness, shedding some light on many aspects of the disease pattern and providing strength to the scientific dissemination about the importance of the social responsibility involved in quarantine measures. after all, apparently, although other epidemics may arise in the future, more or less severe than that caused by sars-cov-2, the results of such natural phenomena, in terms of the number of infected and dead individuals, depend essentially on human behavior and the priority given to the processes of reducing susceptibility. the results obtained from modeling the sars-cov-2 epidemic evolution in brazil allow one to draw up estimates and predictions for the future scenario of the disease progress in the country. as discussed, both scenarios -the worrying and the controlable -are possible and compatible with the current data. in this context, dissemination of scientific facts and awareness-raising campaigns are of paramount worthness, shedding some light on the importance of isolation policies during epidemic situations. in this article, we reformulated the sir model to comply with the hypotheses of a susceptible population that grows over time and varies with mortality and birth rates. as well as being able to model susceptibility reductions in function of social measures for controling the epidemic advance. we explored the case of the epidemic evolution in brazil, a worth issue since it could mean, given the characteristics of the country, a considerable impact on the global economy, not to mention the serious consequences to the country's economic and social structure. we conclude that, within the social and economic possibilities of the country, it is prudent to foster the maintenance of quarantine policies in order to avoid mass contamination of the population in april, 2020. nevertheless, the daily updating of data linked to the current situation of the country must be perpetuated, since, for many reasons, it is possible that, to the date, the number of cases are underestimated and, thus, the forecasts provided here may change significantly due to new updates of the real situation in the country. ti = input ('enter the start time value: '); n = input ('enter the number of subdivisions of the time range: '); dt = (tf-ti)/n; t = ti:dt:tf; % constants alpha = input ('enter the average value of the contamination rate: '); gamma = input ('enter the current death rate value: ') beta = input ('enter the average recovery rate: '); d = input ('enter the number of initial patients: '); p(1) = input ('enter the starting value of the percentage of the population free from contamination: '); deltap = input ('enter the value of the percentage reduction of the contamination-free population per day: '); n = input ('enter the population value: '); k(1) = input ('enter the period until 20% of the population is quarantined: '); k(2) = input ('enter the period until 25% of the population is quarantined: '); k(3) = input ('enter the period until 30% of the population is quarantined: '); k(4) = input ('enter the period until 40% of the population is quarantined: '); k(5) = input ('enter the period until 45% of the population is quarantined: '); %initial conditions s(1) = n; r(1) = 0; i(1) = d; %evolution of the susceptible population for i=1:n p(i+1) = p(1)*power((1-deltap),(ti + i*dt)) if (p(i+1) < 0.1) p(i+1) = 0 end end %iteration for i=1:n if (i< round(k(1)/dt)) sder(i) = ((-alpha*i(i)*(s(i)*(1-p(i))))/n)-((gamma-theta)*s(i)); rder(i) = beta*i(i); ider(i) = (((alpha*i(i))*(s(i)*(1-p(i))))/n)-(beta*i(i)); r(i+1) = r(i) + rder(i)*dt; i(i+1) = i(i) + ider(i)*dt; ylabel ('recovered people (n o of people)') sobre a possibilidade de interrupção da epidemia pelo coronavírus (covid-19) com base nas melhores evidências científicas disponíveis plano de contingência do estado de são paulo para infecção humana pelo novo coronavírus -2019-ncov. secretaria de estado da saúde modelos matemáticos aplicadosà epidemiologia. faculdade de economia universidade do porto, tese de mestrado essential mathematical biology mathematical epidemiology population biology of infectious disease: part i secretaria estadual de saúde do rio grande do sul as medidas de quarentena humana na saúde pública: aspectos bioéticos department of economic and social affairs, population division genoma do sars-cov-2 do primeiro caso de covid-19 da américa latina sequenciado em 48 horas pelo instituto adolfo lutz coronavírus: 18 mortes e 1.128 casos confirmados coronavírus cases: brazil s(i+1) = (s(i) + sder(i)*dt) else if (i > round(k(1)/dt)) && (i < round(k(2)/dt)) i)-0.2)))/n)-((gamma-theta)*s(i) rder(i) = beta*i(i) i))*(s(i)*(1-p(i)-0.2)))/n)-(beta*i(i) r(i+1) = r(i) + rder(i)*dt i(i+1) = i(i) + ider(i)*dt s(i+1) = (s(i) + sder(i)*dt) else if (i > round(k(2)/dt)) && (i < round(k(3)/dt)) i)-0.25)))/n)-((gamma-theta)*s(i) rder(i) = beta*i(i) i))*(s(i)*(1-p(i)-0.25)))/n)-(beta*i(i) r(i+1) = r(i) + rder(i)*dt i(i+1) = i(i) + ider(i)*dt s(i+1) = (s(i) + sder(i)*dt) else if (i > round(k(3)/dt)) && (i < round(k(4)/dt)) sder(i) = ((-alpha*i(i)*(s(i)*(1-p(i)-0.3)))/n)-((gamma-theta)*s(i)) rder(i) = beta*i(i) i))*(s(i)*(1-p(i)-0.3)))/n)-(beta*i(i) r(i+1) = r(i) + rder(i)*dt i(i+1) = i(i) + ider(i)*dt s(i+1) = (s(i) + sder(i)*dt) else if (i > round(k(4)/dt)) && (i < round(k(5)/dt)) sder(i) = ((-alpha*i(i)*(s(i)*(1-p(i)-0.4)))/n)-((gamma-theta)*s(i)) rder(i) = beta*i(i) i))*(s(i)*(1-p(i)-0.4)))/n)-(beta*i(i) r(i+1) = r(i) + rder(i)*dt i(i+1) = i(i) + ider(i)*dt s(i+1) = (s(i) + sder(i)*dt) i)*(1-p(i)-0.45)))/n)-((gamma-theta)*s(i) rder(i) = beta*i(i) i))*(s(i)*(1-p(i)-0.45)))/n)-(beta*i(i) r(i+1) = r(i) + rder(i)*dt i(i+1) = i(i) + ider(i)*dt s(i+1) = (s(i) + sder(i)*dt) i(1) for i=2:tf i_per_day(i) = i(i*(1/dt)) end plot (t_in_days,i_per_day) title ('infected x time') xlabel ('time (days)') ylabel s_per_day (1) = s(1) for i=1:tf if (i< round(k(1)/dt)) s_per_day(i) = s(i*(1/dt))*(1-p(i*(1/dt))) else if (i > round(k(1)/dt)) && (i < round(k(2)/dt)) /dt))*(1-p(i*(1/dt))-0.2) else if (i > round(k(2)/dt)) && (i < /dt))*(1-p(i*(1/dt))-0.25) else if (i > round(k(3)/dt)) && (i < /dt))*(1-p(i*(1/dt))-0.30) else if (i > round(k(4)/dt)) && (i < /dt))-0.40) else s_per_day(i) = s(i*(1/dt))*(1-p(i*(1/dt))(t_in_days,s_per_day) title ('susceptible x time') xlabel ('time (days)') i=1:tf r_per_day(i) = r(i*(1/dt)) end plot (t,r) title the algorithm used to solve the system of ode's was formulated in mat lab language, and it is configured as follows:%algorithm: covid-19 in brazil %domain tf = input ('enter the ending time value: '); key: cord-011411-hufxjf5p authors: oliveira, thalita evani silva; pelaquim, isadora fernanda; flores, eduardo furtado; massi, rodrigo pelisson; valdiviezo, milton james jiménez; pretto‐giordano, lucienne garcia; alfieri, amauri alcindo; saut, joão paulo elsen; headley, selwyn arlington title: mycoplasma bovis and viral agents associated with the development of bovine respiratory disease in adult dairy cows date: 2019-06-24 journal: transbound emerg dis doi: 10.1111/tbed.13223 sha: doc_id: 11411 cord_uid: hufxjf5p the etiology and pathologic findings of bovine respiratory disease (brd) in adult dairy cows (n = 35) from a commercial dairy herd in southern brazil were investigated. pulmonary samples were examined for histopathologic patterns and specific features within these patterns, while immunohistochemical (ihc) assays were designed to detect the intralesional antigens of viral infectious disease agents and mycoplasma bovis. pneumonia was diagnosed in 91.4% (32/35) of these cases; neither pneumonia nor any of the infectious disease pathogens evaluated occurred in three cows. the presence of multiple respiratory pathogens in 75% (24/32) of these cases indicated the complex origin of pneumonia in cattle. interstitial pneumonia, necrosuppurative bronchopneumonia and suppurative bronchopneumonia were the principal patterns of pulmonary disease identified by histopathology. the most frequent pathogens identified by ihc were bovine viral diarrhea virus (bvdv; n = 18), m. bovis (n = 16) and bovine alphaherpesvirus type 1 (bohv‐1; n = 14), followed by bovine respiratory syncytial virus (brsv; n = 11) and bovine parainfluenza virus type 3 (bpiv‐3; n = 5). obliterative bronchiolitis and peribronchial lymphocytic cuffings were the characteristic histopathologic features associated with m. bovis. necrohemorrhagic bronchitis with bronchial angiogenesis was associated with bohv‐1. necrotizing bronchitis and bronchiolitis were associated with bvdv, bohv‐1 and brsv. ballooning degeneration of the bronchial and bronchiolar epithelia was associated with brsv and bohv‐1. this is the first report from brazil that correlated the histopathologic findings of brd with the associated infectious disease agents by immunohistochemistry. m. bovis was frequently detected in the tissues of cows with fatal pulmonary disease during this study and may be a possible primary disease pathogen associated with the development of brd in dairy cows. additionally, the histopathologic features identified within patterns of pulmonary disease during this investigation may be an efficient diagnostic tool to associate histopathologic findings with specific agents of brd in dairy cows. the bovine respiratory disease (brd) is a multifactorial and multiaetiological disease associated with several infectious disease agents panciera & confer, 2010) . data relative to the occurrence of brd in brazil are scarce and incipient. most of these investigations used polymerase chain reaction (pcr) and identified infectious agents of brd such as histophilus somni (headley, alfieri, oliveira, beuttemmuller, & alfieri, 2014; headley et al., 2018) , bovine alphaherpesvirus type 1, bohv-1 (suarez heinlein et al., 1993) , bovine respiratory syncytial virus, brsv (arns et al., 2003; headley et al., 2017) , bovine viral diarrhea virus, bvdv (cortez et al., 2006; flores, ridpath, weiblen, vogel, & gil, 2002; otonel et al., 2014; silveira et al., 2017) , bovine coronavirus, bcov (headley et al., 2018) , pasteurella multocida headley et al., 2018) , mannheimia haemolytica headley et al., 2018) and mycoplasma bovis (tortorelli et al., 2017) . furthermore, studies done in brazil using serology identified seropositivity to infectious disease agents including bohv-1 (barbosa, brito, & alfaia, 2005; fernandes, pimenta, pituco, brasil, & azevedo, 2016) , bovine parainfluenza virus type 3, bpiv-3 (gonçalves et al., 2003) , brsv (driemeier et al., 1997) , and bvdv (flores et al., 2005; wageck canal, strasser, hertig, masuda, & peterhans, 1998) and m. bovis (pretto et al., 2001) . additionally, there is the isolation of m. bovis (pretto et al., 2001) , while few studies from brazil have investigated only brsv by immunohistochemistry, ihc (brasil et al., 2013; peixoto et al., 2000) . the detection of antigen-coding sequences in tissues by pcr in the absence of histopathologic findings does not necessarily indicate that the identified agent is associated with a specific lesion or disease (maes et al., 2013) . disease due to infectious agents associated with brd is confirmed by the simultaneous presence of pathogens within the affected tissues (fulton & confer, 2012) . the ihc assay is a sensitive diagnostic technique that can be used to identify the intralesional presence of specific protein of infectious disease agents associated with histopathologic lesions in formalin-fixed paraffin embedded (ffpe) tissues sections (fulton & confer, 2012; maes et al., 2013) , and the results obtained are strong evidence of an associated disease process within the affected tissues (fulton & confer, 2012) . the disease pathogens associated with brd have been evaluated extensively mainly in north america (fulton, 2009; fulton et al., 2009; panciera & confer, 2010; wolfger, timsit, white, & orsel, 2015) and australia (cusack, mcmeniman, & lean, 2003; hay, morton, mahony, clements, & barnes, 2016) . however, only a few studies have used histopathologic diagnosis with related ihc assays to confirm the participation of infectious disease agents associated with brd (gershwin et al., 2015; haines, martin, clark, jim, & janzen, 2001; haines et al., 2004; rodríguez, bryson, ball, & forster, 1996) . this study describes the histopathologic patterns with associated histologic features and the ihc findings associated with m. bovis and four viral agents of brd in a commercial dairy herd from southern brazil. this study investigated the occurrence of infectious disease agents of brd and the pathologic findings in holstein cows (n = 35) from a commercial dairy establishment in eastern central paraná, southern brazil. this establishment consisted of 1,500 holstein dairy cows with milk production of 45,000 l/day and an average of 29.2 l/cow/ day. due to the purchase of heifer and cows from different neighbouring herds, as well as from farms from neighbouring cities, this farm is considered as an open dairy cattle herd. between january and september 2017, there were reports of recurrent respiratory distress of the affected dairy cows that demonstrated clinical signs of inappetence, reluctance to walk and pulmonary distress (dyspnea, extended head and neck, and audible noise when breathing) associated with brd, and eventually died spontaneously. respiratory diseases were predominant in recently calved cows that demonstrated low morbidity (10%; 150/1,500) and mortality (2.3%; 35/1,500). autopsies were performed by on-site veterinarians during this seven-month period as mortality occurred; pulmonary samples were collected and submitted for laboratory diagnosis after autopsy. the clinical course of the respiratory disease and possible antibiotic therapies are not known. refrigerated pulmonary sections were submitted for pathologic diagnostics; tissues sections were fixed by immersion in 10% buffered formalin solution for 24 hr and then routinely processed for histopathologic evaluation with the haematoxylin and eosin (h&e) stain. histopathologic patterns were classified (teso, sah) and recorded according to the presence/absence of bronchopneumonia (suppurative, necrosuppurative, fibrinous or fibrinosuppurative) and interstitial pneumonia. additionally, the occurrence of specific histopathologic features associated with these patterns of pulmonary disease such as obliterative bronchiolitis, syncytial formation, necrotizing bronchitis/bronchiolitis/alveolitis, necrohemorrhagic bohv-1, bovine pulmonary mycoplasmosis, bovine respiratory syncytial virus, bovine viral diarrhea virus, diagnostic immunohistochemistry, interstitial pneumonia, respiratory pathogens bronchiolitis, abscesses and intralesional bacterial accumulations was identified and recorded. furthermore, whenever necessary new histologic slides were evaluated with the brown-brenn modified staining technique to detect gram-positive or gram-negative bacteria, the giemsa stain was used to detect intralesional accumulations of mycoplasma spp. immunohistochemistry assays were performed on lung sections to investigative the presence of five pathogens associated with brd: bohv-1, brsv, bvdv, bpiv-3 and m. bovis. selected ffpe tissue sections from the lung of each cow were prepared on silanized slides with polyl-lysine 0,1% (sigma-aldrich, st. louis, mo, usa), deparaffinized, hydrated in alcohol baths and subjected to antigen retrieval. the dilutions of the monoclonal antibodies used during this investigation are shown in table 1 . antigen retrieval (table 1 ) was achieved by using citrate buffer (ph 6.0) or tris-edta buffer with 0.05% tween (ph 9.0). both solutions were utilized with the pressure cooker system (electrolux pressure cooker pcc10, são paulo, brazil) for 5 min. endogenous peroxidase was blocked with distilled water and hydrogen peroxide (6%) for 30 min in a dark chamber. the primary incubation was achieved with the monoclonal antibodies shown in table 1 (oliveira, lorenzetti, alfieri, & lisbôa, 2015) , bvdv (lunardi, headley, lisboa, amude, & alfieri, 2008) and m. bovis (pretto et al., 2001) ; positive controls for bpiv-3 were obtained from tissue culture maintained within our laboratory. negative control consisted of using the same tissue, with substitution of the primary antibody by its diluent. positive and negative controls were included in each ihc assay. an overview of the principal histopathologic patterns of pulmonary disease observed in adult dairy cows during this study and their associated histologic features are given in table 2 . pneumonia was diagnosed in 91.4% (32/35) of the affected cows, and at least one infectious disease agent was identified in each animal by ihc (table 3) ; however, agents associated with brd were not identified in 8.6% (3/35) of cows without pneumonia. interstitial pneumonia (46.8%; 15/32) was the most predominant pattern of pulmonary disease observed, followed by necrosuppurative bronchopneumonia (28.1%; 9/32; figure 1a ) with peribronchial lymphocytic cuffings (21.9%; 7/32), and suppurative bronchopneumonia (18.7%; 6/32). additionally, two cows without histopathologic evidence of pneumonia had necrotizing bronchitis. accumulations of intralesional, giemsa-stained, coccoid bacteria were associated with necrosuppurative and suppurative bronchopneumonia; gram-positive or gram-negative bacteria were not detected by the modified brown-brenn stain. the histopathologic features associated with the patterns of pneumonia are summarized in table 3 ; these lesions included obliterative bronchiolitis (28.6%; 10/35; figure 1b) , necrotizing bronchitis (18.7%; 6/32) and bronchiolitis (12.5%; 4/32; figure 1c ta b l e 1 list of antibodies, dilutions, method of antigen retrieval and source manufactures of the immunohistochemical assays epithelia, hyperplasia of type ii pneumocytes (6.2%; 2/32) and necrohemorrhagic bronchitis with angiogenesis at the lamina propria of the bronchus (6.2%; 2/32; figure 1f ). during this investigation, singular and mixed infections were identified (table 4 ). however, dual (31.3%; 10/32) and triple (18.7%; 6/32) associations were the most frequent forms at this outbreak, followed by quadruple (6.3%; 2/32) and quintuple (3.1%; 1/32, cow #34) simultaneous association of infectious disease agents associated with brd. singular infections were caused by bvdv (15.6%; 5/32), m. bovis (12.5%; 4/32), brsv (9.4%; 3/32) and bohv-1 (3.1%; 1/32); singular infections were not associated with bpiv-3. all antibodies demonstrated cytoplasmic immunolabelling within epithelial cells of bronchi and/or bronchioles of the infected cows. when the histopathologic patterns were correlated with the ta b l e 3 principal histopathologic diagnosis/features and immunohistochemical findings of bovine respiratory disease in 32 dairy cows obliterative bronchiolitis m. bovis (10/10) primary pulmonary infections due to bvdv were demonstrated experimentally (fulton et al., 2016; gershwin et al., 2015; rodríguez et al., 1996) and observed in field outbreaks of brd (fulton et al., 2000 (fulton et al., , 2004 szeredi, janosi, & palfi, 2010 in coinfections (ridpath, 2010) . this aspect is relevant not only for the interpretation of experimental data, but because bvdv may interact with m. bovis in field conditions (bürgi et al., 2018) . additionally, some strains of bvdv are immunosuppressive in cattle, due to the loss of alveolar macrophage functionality (bürgi et al., 2018; welsh, adair, & foster, 1995) and severe and extensive apoptosis of lymphocytes (chase, 2013) . consequently, immunosuppression due to bvdv associated with bohv-1, brsv and m. bovis may have resulted in an increased severity of disease in this dairy herd, due to incapacity of the innate immune system to control these infections. in our study, several chondrocytes of the hyaline cartilage of the bronchus demonstrated positive immunoreactivity for brsv, bohv-1 and bvdv, with diffused immunoreactivity to bvdv occurring within the chondrocytes of two cows. similar positive immunoreactivity to bvdv was described in 60% (6/10) of persistently infected (pi) calves, where it was proposed that the presence of bvdv antigen in respiratory cartilage is an indication that this viral disease pathogen predisposes cows to secondary bacterial infection (confer, fulton, step, johnson, & ridpath, 2005) . in the cases herein described, we were unable to confirm these cows as being pi animals since two biological samples were not available for testing. however, there was positive immunoreactivity to bvdv (using mab 15c5) within the chondrocytes of the hyaline cartilage of the bronchus of the fetus of one of these cows. collectively, these findings may suggest that the fetus of the gravid cow and probably the cow itself were pi animals; moreover, positive immunoreactivity to bvdv within the pulmonary cartilage of these two cows can correlate with the occurrence of simultaneous infections in these animals (confer et al., 2005) . additionally, it must be highlighted that the mab used during this study to identify intralesional antigens of bvdv has elevated specificity and sensitivity for the diagnosis of this infectious disease pathogen (haines, clark, & dubovi, 1992) . the first identified m. bovis-associated pulmonary disease in 26.1% (12/46) of calves due to a combination of bacterial culture and direct immunofluorescence using lung sections (pretto et al., 2001) . while the other amplified nucleic acids of m. bovis from 5.6% (1/18) of nasal swabs from dairy cows (tortorelli et al., 2017) . the marked difference between these and the current study was the confirmation of disease (fulton & confer, 2012) , in our investigation due to the innecrosuppurative bronchopneumonia and peribronchial lymphocytic cuffings are the hallmarks of chronic pulmonary mycoplasmosis in cattle (nicholas & ayling, 2003) and calves (hermeyer et al., 2012; khodakaram-tafti & lópez, 2004) , and were the main findings observed in the affected dairy cows during this study. these findings were previously described (caswell & archambault, 2007; gagea et al., 2006; haines et al., 2004) and demonstrate the ability of m. bovis to invade the pulmonary parenchyma, as was observed in experimental (gershwin et al., 2015; hermeyer et al., 2012; rodríguez et al., 1996; thomas, howard, stott, & parsons, 1986 ) and spontaneous (gagea et al., 2006) cases of pulmonary disease in cattle. furthermore, m. bovis may induce cytotoxicity and induction of apoptosis of the alveolar macrophage (bürgi et al., 2018) , and neutrophils, inhibit the production of nitric oxide in cows (jimbo et al., 2017) and infects a wide range of epithelial and immune cells (bürki, frey, & pilo, 2015) . these mechanisms then favour the dissemination of m. bovis and would have facilitated simultaneous infections in this herd with bvdv, bohv-1 and brsv. the silent immunomodulatory and immunosuppressive effects of m. bovis predisposes the respiratory tract of calves to other bacterial infections (margineda et al., 2017; nicholas, 2011; poumarat et al., 2001) . these effects have been demonstrated experimentally (poumarat et al., 2001; rodríguez et al., 1996; vanden bush & rosenbusch, 2003) and were described in spontaneous cases (haines et al., 2004; rodríguez et al., 1996; yi̇lmaz et al., 2016) , and there are reports of pneumonic diseases in which m. bovis was the only pathogen identified (gershwin et al., 2015; nicholas, 2011) . these findings may suggest that m. bovis can act as a primary disease pathogen and produce brd. however, the possibility of m. bovis being a primary disease agent is still controversial, since this agent may colonize and f i g u r e 3 immunohistochemical findings observed in dairy cattle with bovine respiratory disease. (a) there is positive immunoreactivity to antigens of bohv-1 ballooning degeneration of the bronchiole (black arrows) and endothelial staining in alveolar capillaries (white arrows). (b) there is positive immunoreactivity for bvdv at the endothelium of alveolar venule (black arrows), within degenerated endothelial cells (white arrows), and (c) necrotizing bronchiolitis (arrow). (d) observe positive immunoreactivity for antigens of brsv at the bronchial epithelium, within detached bronchial epithelial cells (arrow), in bronchial hyaline cartilage (asterisk). (e) observe positive immunolabelling for antigens of bvdv at the bronchial epithelium and within chondrocytes of the bronchial hyaline cartilage (asterisk). (f) there is positive immunoreactivity associated with bohv-1 at the bronchial epithelium of a cow with diffused ulcerative bronchitis and epithelial necrotizing bronchitis (arrows heads), at the newly formed capillaries (arrows) and mixed peribronchial glands (asterisks). immunoperoxidase counterstained with haematoxylin. bar, a-c, e 50 μm; d, f 200 μm as far as the authors are aware, this manuscript may represent the first description of m. bovis-related brd in dairy cows. this pathogen was frequently associated with several disease syndromes in dairy calves (mahmood et al., 2017) and feedlot cattle (caswell & archambault, 2007; haines et al., 2001) , including descriptions of m. bovis-related pneumonia (gagea et al., 2006; mahmood et al., 2017 ), but we did not locate reports of m. bovis-induced brd in adult dairy cows on searching major databases. furthermore, m. bovis was not identified in recent studies done by our group to identify this pathogen associated with brd in feedlot cattle from different geographical regions of brazil headley et al., 2014 headley et al., , 2018 . additionally, there are only two reports (pretto et al., 2001; tortorelli et al., 2017) of m. bovis-associated pulmonary disease in cattle from this country. although the exact reasons for the low detection rate of m. bovis-associated brd in brazil are unknown, we believe that the reduced identification of this agent may be related to the diagnostic strategy used and the type of cattle evaluated, that is beef against dairy. all previous cases of m. bovis-associated brd were diagnosed in dairy cows (pretto et al., 2001; tortorelli et al., 2017) , while this bacterial pathogen was not identified in studies done with beef cattle (headley et al., , 2017 (headley et al., , 2018 . it must be highlighted that nasal swabs were tested by pcr in the beef cattle surveys done by our group which resulted in negative results; however, these negative results could have been associated with the sporadic elimination of m. bovis so that pcr testing would not be an efficient method to detect this pathogen (nicholas, 2011) . this sporadic shedding of m. bovis may also explain the low results (5.6%; 1/18) obtained in a study done by another group from brazil that used the same molecular testing strategy in dairy cattle (tortorelli et al., 2017) , as compared with the elevated results (26.1%; 12/46) obtained by bacterial culture and immunofluorescence assay using pulmonary tissue with characteristic lesions (pretto et al., 2001) . since pulmonary mycoplasmosis is a chronic disease (caswell & archambault, 2007) , dairy cows that are maintained for longer dura(nicholas & ayling, 2003) , the sporadic shedding of m. bovis (nicholas, 2011) in affected cows, and the molecular testing frequently used to identify this pathogen in association with brd. consequently, this pathogen should be suspected in dairy cows with clinical manifestations of respiratory distress and be included in the differential diagnosis of infectious disease agents associated with brd in adult dairy cattle from brazil. moreover, pulmonary tissue rather than nasal swabs may be more efficient to diagnose m. bovis in dairy cattle. necrohemorrhagic bronchitis with bronchial angiogenesis was exclusively associated with infections induced by bohv-1 in this study. we have not seen this lesion previously described in the deby bohv-1 is not fully elucidated, these cytokines may be associated with the development of this lesion due to inflammatory reaction, and necrosis; in addition, il-8 has angiogenic and repair qualities (koch et al., 1992) . consequently, further studies are needed to understand the pathophysiology and the importance of this unique lesion. few studies have demonstrated synergism of brsv with bvdv (liu et al., 1999) , h. somni (agnes et al., 2013; headley et al., 2017) and m. bovis (thomas et al., 1986) . experimentally it was demonstrated that this synergism induced alveolar cell retraction and increased degradation of collagen by tnfα (agnes et al., 2013) . both mechanisms may facilitate pulmonary damage resulting in subsequent pneumonia and the dissemination of the infectious pathogen (agnes et al., 2013) . additionally, brsv infects type i and type ii pneumocytes (bryson, mcconnell, mcaliskey, & mcnulty, 1991) , with consequent apoptosis to these cells (viuff et al., 2002) , and produces necrosis of alveoli and small airways (bryson et al., 1991) , due to alveolar neutrophilic exudation (agnes et al., 2013) , resulting in suppurative alveolitis/bronchiolitis and necrotizing bronchiolitis/bronchitis (andrews & kennedy, 1997; brasil et al., 2013; gershwin et al., 2015; peixoto et al., 2000) . moreover, during this investigation, hyperplasia of type ii pneumocytes was observed in association only with positive immunoreactivity to brsv; similar findings were previously associated with chronic epithelial injury in the proximal alveolar region (barry, miller, & crapo, 1985) and identified in beef cattle with chronic pulmonary disease (driemeier et al., 1997) . the low number of cases with syncytial formation (4/11) in the present study may be due to the fact that the manifestations were chronic (driemeier et al., 1997) . these histopathologic findings were observed in cattle infected by brsv during this investigation and may have contributed to the increased severity of pulmonary lesions observed in the dairy cows herein described. this is the first report from brazil that demonstrated and correlated the histopathologic findings of bovine respiratory disease by immunohistochemistry. necrosuppurative bronchopneumonia, obliterative bronchiolitis and peribronchial lymphocytic cuffings were the characteristic histopathologic features associated with mycoplasma pneumonia. necrotizing bronchitis and bronchiolitis were associated with bvdv, bohv-1 and brsv. necrohemorrhagic bronchitis with bronchial angiogenesis was associated with infection by bohv-1. m. bovis was commonly detected in the tissues of fatal pulmonary disease during this outbreak and may be a possible primary disease pathogen associated with the development of bovine respiratory disease. moreover, the histopathologic features observed within the patterns of pulmonary disease may be an excellent diagnostic tool to identify some infectious disease agents of brd in dairy cattle. the authors are grateful for the monoclonal antibody against bvdv massi, rp and valdiviezo, mjj are recipients of capes fellowships. the authors declared no potential conflicts of interest with respect to the research, authorship and/or publication of this article. bovine respiratory syncytial virus and histophilus somni interaction at the alveolar barrier respiratory diagnostic pathology. veterinary clinics of north america: food animal practice characterization of bovine respiratory syncytial virus isolated in brazil bovine respiratory disease complex associated mortality and morbidity rates in feedlot cattle from southeastern brazil seroprevalence and risk factors to the infectious by bovine herpesvirus type 1 (bhv-1) in goiás state, brazil (in portuguese) effects of inhalation of 0.12 and 0.25 parts per million ozone on the proximal alveolar region of juvenile and adult rats respiratory diseases in calves in southern rio grande do sul: study of 33 outbreaks ultrastructural features of alveolar lesions in induced respiratory syncytial virus pneumonia of calves mycoplasma bovis co-infection with bovine viral diarrhea virus in bovine macrophages virulence, persistence and dissemination of mycoplasma bovis mycoplasma bovis pneumonia in cattle mycoplasma bovis in respiratory disease of feedlot cattle. veterinary clinics of north america: food animal practice the impact of bvdv infection on adaptive immunity viral antigen distribution in the respiratory tract of cattle persistently infected with bovine viral diarrhea virus subtype 2a genetic characterization of brazilian bovine viral diarrhea virus genetic characterization of brazilian bovine viral diarrhea virus isolates by partial nucleotide sequencing of the 5′-utr region the medicine and epidemiology of bovine respiratory disease in feedlots clinic-pathological aspects in the natural infection of bovine respiratory syncytial virus (brvs) in extensive management of cattle in rio grande do sul risk factors associated with bohv-1 and bvdv seropositivity in buffaloes (bubalus bubalis) from the state of paraiba, northeastern brazil phylogenetic analysis of brazilian bovine viral diarrhea virus type 2 (bvdv-2) isolates: evidence for a subgenotype within bvdv-2 bovine viral diarrhea virus (bvdv) infection in brazil: history, current situation and perspectives bovine respiratory disease research lung pathology and infectious agents in fatal feedlot pneumonias and relationship with mortality, disease onset, and treatments maternally derived humoral immunity to bovine viral diarrhea virus (bvdv) 1a, bvdv1b, bvdv2, bovine herpesvirus-1, parainfluenza-3 virus bovine respiratory syncytial virus, mannheimia haemolytica and pasteurella multocida in beef calves, antibody decline by half-life studies and effect on response to vaccination laboratory test descriptions for bovine respiratory disease diagnosis and their strengths and weaknesses: gold standards for diagnosis, do they exist? detection and characterization of viruses as field and vaccine strains in feedlot cattle with bovine respiratory disease bovine viral diarrhea viral infections in feeder calves with respiratory disease: interactions with pasteurella spp., parainfluenza-3 virus, and bovine respiratory syncytial virus naturally occurring mycoplasma bovis-associated pneumonia and polyarthritis in feedlot beef calves single pathogen challenge with agents of the bovine respiratory disease complex isolation of bovine parainfluenza virus type 3 in rio grande do sul, brazil (in portuguese) monoclonal antibodybased immunohistochemical detection of bovine viral diarrhea virus in formalin-fixed, paraffin-embedded tissues the immunohistochemical detection of mycoplasma bovis and bovine viral diarrhea virus in tissues of feedlot cattle with chronic, unresponsive respiratory disease and/or arthritis immunohistochemical study of hemophilus somnus, mycoplasma bovis, mannheimia hemolytica, and bovine viral diarrhea virus in death losses due to myocarditis in feedlot cattle associations between animal characteristic and environmental risk factors and bovine respiratory disease in australian feedlot cattle histophilus somni is a potential threat to beef cattle feedlots in brazil bovine respiratory disease associated with histophilus somni and bovine respiratory syncytial virus in a beef cattle feedlot from southeastern brazil molecular survey of infectious agents associated with bovine respiratory disease in a beef cattle feedlot in southern brazil chronic pneumonia in calves after experimental infection with mycoplasma bovis strain 1067: characterization of lung pathology, persistence of variable surface protein antigens and local immune response effect of mycoplasma bovis on bovine neutrophils. veterinary immunology and immunopathology immunohistopathological findings in the lungs of calves naturally infected with mycoplasma bovis interleukin-8 as a macrophagederived mediator of angiogenesis synergistic effects of bovine respiratory syncytial virus and non-cytopathic bovine viral diarrhea virus infection on selected bovine alveolar macrophage functions outbreak of acute bovine viral diarrhea in brazilian beef cattle: clinicopathological findings and molecular characterization of a wild-type bvdv strain subtype 1b beyond h&e: integration of nucleic acidbased analyses into diagnostic pathology patho-bacteriological investigation of an outbreak of mycoplasma bovis infection in calves -emerging stealth assault mycoplasma bovis pneumonia in feedlot cattle and dairy calves in argentina bovine mycoplasmosis: silent and deadly mycoplasma bovis: disease, diagnosis, and control prevalence of latent infection with bohv-1 and bohv-5 in beef cattle of parana, brazil (in portuguese) the diversity of bvdv subgenotypes in a vaccinated dairy cattle herd in brazil pathogenesis and pathology of bovine pneumonia. veterinary clinics of north america: food animal practice spontaneous brsv infection in cattle of the state of alagoas, brazil spontaneous brsv infection in cattle of the state of alagoas, brazil (in portuguese). pesquisa veterinária brasileira efficacy of spectinomycin against mycoplasma bovis induced pneumonia in conventionally reared calves mycoplasma bovis isolation from calves with pneumonia (in portuguese). veterinária notícias the contribution of infections with bovine viral diarrhea viruses to bovine respiratory disease. veterinary clinics of north america: food animal practice bovine herpesvirus type 1 infection of bovine bronchial epithelial cells increases neutrophil adhesion and activation pathological and immunohistochemical studies of natural and experimental mycoplasma bovis pneumonia in calves coinfection with bovine viral diarrhea virus and mycoplasma bovis in feedlot cattle with chronic pneumonia genetic diversity of brazilian bovine pestiviruses detected between molecular characterization of south american bovine herpesvirus-1 isolates with monoclonal antibodies and sds-page microbiological and pathological examination of fatal calf pneumonia cases induced by bacterial and viral respiratory pathogens mycoplasma bovis infection in gnotobiotic calves and combined infection with respiratory syncytial virus evaluation of mollicutes microorganisms in respiratory disease of cattle and their relationship to clinical signs characterization of the immune response to mycoplasma bovis lung infection replication and clearance of respiratory syncytial virus: apoptosis is an important pathway of virus clearance after experimental infection with bovine respiratory syncytial virus detection of antibodies to bovine viral diarrhoea virus (bvdv) and characterization of genomes of bvdv from brazil effect of bvd virus infection on alveolar macrophage functions a systematic review of bovine respiratory disease diagnosis focused on diagnostic confirmation, early detection, and prediction of unfavorable outcomes in feedlot cattle histopathological, immunohistochemical and bacteriological characterization of mycoplasma bovis pneumonia in cattle additional supporting information may be found online in the supporting information section at the end of the article. key: cord-333487-zem2d4y6 authors: thomaz ugliara barone, mark; bega harnik, simone; vieira de luca, patrícia; letícia de souza lima, bruna; josé pineda wieselberg, ronaldo; ngongo, belinda; cordeiro pedrosa, hermelinda; pimazoni-netto, augusto; reis franco, denise; de fatima marinho de souza, maria; carvalho malta, deborah; giampaoli, viviana title: the impact of covid-19 on people with diabetes in brazil date: 2020-07-03 journal: diabetes res clin pract doi: 10.1016/j.diabres.2020.108304 sha: doc_id: 333487 cord_uid: zem2d4y6 abstract the present study aims atidentifying main barriers faced by people living with diabetes in brazil during the covid-19 pandemic. methods in a convenience sampling study, data were collected from 1701 individuals, aged 18 or above; 75.54% female participants; 60.73% t1d and 30.75% t2d, between april 22nd and may 4th, using an anonymous and untraceable survey containing 20 multiple choice questions (socio-demographic; health status and habits of life during covid-19 pandemic). relationship between variables was established using the multiple correspondence analysis technique. results 95.1% of respondents reduced their frequency of going outside of their homes; among those who monitored blood glucose at home during the pandemic (91.5%), the majority (59.4%) experienced an increase, a decrease or a higher variability in glucose levels; 38.4% postponed their medical appointments and/or routine examinations; and 59.5% reduced their physical activity. t1d, the youngest group, was more susceptible to presenting covid-19 symptoms despite not being testing; whilst the td2 group had higher frequency of comorbidities that are additional risk factors for covid-19 severity. conclusions this study provides a firsthand revelation of the severity of covid-19 on individuals with diabetes in brazil, altering their habits, which impacted their glycemia, potentially increasing their risk of poor outcomes if infected by sars-cov-2. the outbreak covid-19 has led to an unprecedented global health crisis which is testing health systems' preparedness and ability to cope with a pandemic response [1] [2] [3] [4] . . brazilexperienced a similar situation. thefirst sars-cov-2 case was officially reported in december 2019 in wuhan,china, and rapidly spread in the entire country and beyond within 30 days [5] [6] [7] . the first suspected case in latin america was reported on january 27th in brazil and the first case confirmed in brazil on february 26th of 2020 [2, 3, 7] . a series of measures were put in place p to prepare brazil for the anticipated health crisis prior to the declaration of covid-19 as being public health emergency of international concern, on january 30th [2] , and then a pandemic, on march 11th [8] . following these international alerts,less than a month after the first confirmed case, on march 20th, the brazilian ministry of health recognized that community transmission was already happening in brazil [2] . infection by sars-cov-2 causes major disruptions and threats ,in addition to the loss of human lives, with case fatality rate ranging from 0.2% in germany, to 7.7%in italy [9] , the impact of covid-19 is beyond imagination and is sparkling a global mourning,booming afeeling of unsafety and uncertainty. on june 9th, according to the world health organization (who), 7,127,753 cases and 407,159 deaths duetocovid-19 were confirmed in 216 countries [10] . fcases and mortality in brazil reached 739,503 and 38,406 respectively,with a case fatality rate of 5.2% [11] . while this is the highest number of cases and one of the highest case fatality rate in latin america [12] , scientists argue that cases and mortality are extremely underscored due to the low number of tests performed among other reasons [1, 4, 12, 13] by possible 14-20 times the official reported figures [14] . authors of the first chinese and italian reports alerted for the worse prognosis of individuals with diabetes and other noncommunicable disease (ncds), in comparison with populations of the same age group without those chronic conditions [5, [15] [16] [17] [18] . further retrospective studies have revealed that, within this group of patients, hyperglycemia was associated with higher severity and mortality rates [15, 19, 20, 21] , for reasons under investigation [22, 23] . additionally, usual comorbidities such as hypertension, cardiovascular disease, older age, and gender (male) also complement increased severity and mortality risks of individuals with diabetes hospitalized due to covid-19 [24] . , with a prevalence as high as 16.8 million people or 11.4% of the population between 20 and 79 years old, brazil is among the top 5 countries with high prevalence of diabetes. diabetes leads g to more than 135,000 deaths yearly [25] . brazil struggles with the continuous treatment routine of impacted populations; only 28.8% are considered to be in target, having a glycated hemoglobin a1c below 7.0% (53mmol/mol) [26] . consequently, 71.2% of brazilians with diabetes belong to a subgroup more exposed to hyperglycemia , which makes them vulnerable to even higher risk of poor outcomes when infected by the sars-cov-2 virus. this state of affairs calls fordeep commitments from the public health in all its forms and a concrete alignment with the who. unfortunately, in the midst of the fight against this novel virus, brazil experienced a troublesome atmosphere of political disputes, blinding authorities to make swift decisions aligned with the global technical recommendations [1, 4, 12] . this also harmed adjustments to continue the proper follow-up and management of other diseases, including both communicable and ncds. for these reasons, the present study aims to investigate challenges encountered by people living with diabetes in brazil during the covid-19 pandemic. data from individuals with diabetes were collected through an anonymous and untraceable survey containing 20 multiple choice questions in portuguese. the authors shared this survey on social media including facebook, through their affiliated institutions, co-ligated or partner entities, and diabetes social media groups. hence, the convenience sampling nature of this study. in addition to being a person living with diabetes, individuals needed to be legally adults (above 18 years old) and accept the terms to share anonymous and untraceable answers. survey responses were collected from april 22nd through may 4th. the first question provided a complete overview of the questionnaire and required confirmation of the heath conditon (diabetes) by the respondent. . this was followed by socio-demographic questions related to age, gender, state of residence, capital/country/coast, education level, number of people living in the household, and nature of the health system which could be public, private or both. subsequent questions served to identify the health status of the participants, asking about diabetes type, and presence and type of comorbidity. all remaining questions covered aspects attributed to the covid-19 pandemic: frequency of going outside, strategies to protect from infection when outside, noted changes in the glycemic levels, access to medical care, changes in eating habits and physical activity, changes in smoking and drinking habits, and suspected or confirmed covid-19 infection by the respondent or cohabitant family member. at the end of the survey, the respondent could leave a comment. several questions and their answers were regarding subjective perceptions, such as "my blood glucose increased", "i am eating more" or "i am exercising much less" than before the pandemic. therefore, answers should not be interpreted as objective measurements, but as subjective comparisons with the prepandemic states. a multivariate analysis of dimensions of covid-19 and types of diabetes (type 1 diabetes -t1d; type 2 diabetes -t2d; others: lada, mody, gestational; and unknown) was performed with multiple correspondence analysis (mca) in r (version 3.6.1) and rstudio (version 1.1.453) [27] . the survey was answered by 1701 individuals, 75.54% were female respondents, 70.78% between 18 and 50 years old, 64.96% of respondents were from southeast of brazil, and the main diabetes types were type 1 (60.73%) and type 2 (30.75%) (full socio-demographic profile in table 1). among the main reported consequences of the covid-19 pandemic were: 95.1% reduced frequency of going outside home (among them, 26.9% never went outside since the beginning of the pandemic); among the ones who monitored their blood glucose at home (91.5%), the majority (59.4%) experienced a deterioration, which included: 31.2% are reporting greater variability than before the pandemic, 20% higher glycemia and 8.2% lower glycemic levels. moreover, 38.4% postponed medical appointments and/or routine exams, and 40.2% did not schedule a medical appointment since the onset of the pandemic. among recommended habits, slated for diabetes treatment, physical activity was most impacted, with a reduction reported by 59.5% of the respondents (14.7% with a slight reduction and 44.8% with a great reduction). see table 2 for habits and behaviors. regarding co-morbidities, for the current study and analysis, we opted to group them into the following: 1) "mental health" which includes the following conditions: depression, anxiety, bulimia, anorexia and diabulimia; and 2) "cardiovascular diseases" comprising : stroke, infarction, hypertension and dyslipidemia. two other groups were already established in the survey as a single answer, which had a parenthesis to facilitate comprehension, the "diabetes related complications" with: retinopathy, neuropathy and diabetic renal disease; and the "respiratory": asthma and copd (table 1) . the analysis revealed the association between age and the occurrence of symptoms of covid-19, type of diabetes and some of the co-morbidities evaluated (figure 1). people with t1d were among the youngest and appeared in proximity to mental health diseases category, but also close to the no-cardiovascular conditions, no-obesity and no-respiratory disease categories. they were alarmingly close to the category that, despite having symptoms of covid-19, had no testing for sars-cov-2. not measuring the blood glucose is close to t2d and unknown diabetes type. t2d, not surprisingly, was more associated than other types with older age, cardiovascular diseases and obesity. it is also worth noting that t2d and older group were the closest to test positive for sars-cov-2. in opposition, individuals who had symptoms of covid-19 and were not tested (125 people or 7.35%) presented higher proximity to increased blood glucose (figure 1 ). measuring blood glucose was related with food consumption and working out, as depicted on figure 2. individuals that experienced decrease in blood glucose levels, increased physical activity and decreased food consumption. meanwhile, higher food consumption and reduced physical activity were associated with higher blood glucose levels. while it seems that the pandemic had a higher impact on habits and glycemic levels of t1d individuals (right side of figure 2), with significant perceived changes, t2d respondents seem to have maintained most of their habits during this period. individuals who exclusively use the brazilian public health system (unified health system -sus), which serves more than 70% of the brazilian population [28] (in our case, 28.16% of the respondents), were who kept venturing out during the pandemic and experienced an increase of blood glucose levels, as shown in figure 3 . t1d individuals were the closest to the use of both health systems (sus and private) and also experienced higher glycemic variability (ups and downs). they had the ability to have friends or relatives to buy or collect their medicines and medical supplies. users of the private health system were closer to experience no glycemic changes during the pandemic, using their own stocks of medicine and medical supplies or ordering for home delivery from private pharmacies (figure 3) . the results above unveil short, mid and long-term risks for individuals with diabetes in brazil. while the federal government and some states made initial commitments and plans [2] , knowing the risks for poor prognosis among individuals living with diabetes and/or other ncds if infected by sars-cov-2. our data revealed that implemented measures did not cover most of this population. the strategy to distribute medicines and medical supplies for 90 days, as recommended by different organizations [29, 30] , in order to avoid monthly trips were effective for only 21% of the 64.5% who received their medication and supplies from sus (or 13.5% of the total respondents). this provision of medicines and supplies for 3 months, avoiding the monthly rounds to public primary healthcare facilities or pharmacies, seemed to be the one of the only specific policies to protect individuals with diabetes and others living with ncds in brazil [31, 32] . although limited, this would at least protect them from encountering infected people seeking care. . meanwhile, at municipality level, certain locations successfully implemented alternative strategies, as hailed by one participant from an inland town: "my town adopted a delivery of medicine method for people with chronic diseases". according to our data, especially individuals w exclusively depended on sus were at higher risk, venturing out of home more often and experiencing an increase in blood glucose levels ( figure 3 ). while differences would not be expected, since brazil prides itself for its universal health coverage, and most people, including the ones with private insurance, rely on sus to receive part or all their medicines and supplies. we hypothesise that this finding highlights the socioeconomic inequalities in the country, which obliges the less privileged to continue going to work during the pandemic and/or to access affordable food. . even though 44.3% of the individuals reported having a family member or friend going monthly to public pharmacies on their behalf to collect medicines and supplies, 49.9% went themselves, perhaps due to lack of direct support.. it is important to highlight that family member's or friend's support may reduce but not eliminate the risk of infection, especially if residing in the same location, acting as a potential vehicle of indirect transmission. another uncomfortable answer came from 5.8% of the individuals who reported halting collection of their medicines and medical supplies and relying on personal stocks, which might be limited in quantity or expected to expire soon. this situation may place those who avoided leaving their homes during the pandemic in a risky untreated situation, a globally shared concern [15, 17, 33, 34, 35] . while it is hard to predict social, economic and health impact of a pandemic, specialists alert to the consequences of implementing only light measures [4, 12, 13, 36, 37, 38] , but, at the same time, also the harmful consequences of lockdowns, mobility restrictions and social distancing on the prevention and control of diabetes and other ncds [17, 34, 39] . barone et al. [39] reported an association between stricter measures against the pandemic and perceived challenges and fear in the diabetes community in south and central american, which, when disconnected from information and educational strategies, would increase the pressure on the health systems [37, 39] . although decentralized (defined by states and municipalities) and delayed [1, 4, 12, 13, 40] , the measures to contain the sars-cov-2 spread in brazil, and reflected on mobility reduction, was experienced by 95.1% of this study's respondents in different degrees (with 26.9% never going outside). differently from kluge et al.'s prediction [17] , in our case it was not associated with increased consumption of alcohol, tobacco and unhealthy foods. notwithstanding, physical activity was affected, being reduced for 59.5% of the respondents. other researchers have also reported physical activity reductions during the pandemic, and alerted for the potential negative consequences on metabolic, cardiovascular and musculoskeletal health [41, 42] . these effects were observed even after short periods of inactivity, are hard to recover and, not only increase premature mortality, but also favors the development of diabetes chronic complications [41, 42] . a strategy to minimize those consequences would be developing good channels and partnerships for informing these populations through the internet and tv broadcasting in a structured manner, focusing on preventive measures and maintenance or improvement of habits and behaviors, such as regular physical activity [17, 34, 41, 42, 43] . this recommendation is compatible with the present findings where 87.4% of the individuals maintained or increased their time watching tv and 90.7% maintained or increased their time on the internet. regarding treatment, the covid-19 pandemic, as predicted and observed by different authors, is impacting availability and access to healthcare professionals (hcps) for the routine care of people with diabetes, since they relocated to emergency rooms, testing sites, icus and other services to attend infected individuals [15, 17, 33, 34, 39] . covid-19 transmission was found to be high among hcps. . we investigated 38.4% of the individuals who postponed their medical appointments and/or examinations. we attributed these results to shortage of hcps, as cited by 3 individuals, reporting appointment cancelation or absence of s physician, or personal decision because of the fear of getting infected at a hospital or clinic. also identified, in other studies as one of the greatest fears of the population [39, 35] . the potential consequence of this phenomenon of fear during the pandemic was reported in a pediatric emergency department, in italy, with reduction and delay in children's arrival, which included cases of severe ketoacidosis and hypoglycemia [35] . although online consultation and other telemedicine strategies were not investigated profoundly in the present study, one of the respondents commented that he/she was having online medical appointments. brazilian laws and regulations became more flexible allowing this type of approach during the covid-19 pandemic [44] . in alignment with other authors and international organizations, we highly recommend it [15, 33, 36, 45, 46, 47, 48] , reinforcing primary healthcare's role during the pandemic through ensuring close and timely monitoring of people with diabetes and other ncds [37, 44, 49] the results show thatall types of diabetes were close to additional risk factors for poor prognosis of individuals infected by sars-cov-2. while t2d and unknown diabetes type (figure 1) appear near other ncds (especially cardiovascular and obesity) [18, 24, 47, 50, 51] , t1d and other types (lada, mody and gestational grouped) presented close proximity to glycemic variability (figure 2) [5, 15, 52] . therefore, we suggest that none of the types should feel safe. although, not surprising, t2d was associated with "50 years and older" (figure 1), and it is known that the covid-19 mortality and severity increase with age [5, 24, 53] .it was unfortunate the proximity of individuals reporting increased blood glucose levels and the presence of covid-19 symptoms without testing (figure 1). the global shortage of tests for sars-cov-2 poses a grand challenge [2] [3] [4] , however, cognizant that high blood glucose increases the risk for infection severity and death [15, 19, 20, 21, 22, 23] , early testing efforts are recommended in this group. in addition, supporting them in intensifying their diabetes self-care practices to quickly bring their glycemia back on track must be prioritized [45, 51, 54] . figure 2 depicts the importance of balancing food and exercise, since individuals who increased or decreased any of them experienced changes in their blood glucose levels, whereas those able to maintain exercise and food consumption avoided glycemic changes. while the present study focused only on diabetes, who's data show that other ncds serviced in similar health systems and pandemic environment, are facing comparable challenges [55] . in terms of unattended needs of individuals with diabetes during this covid-19 crisis, brazil is not the only country with unaddressed demands. in a collection of testimonials from people with diabetes in different countries, the international diabetes federation exposed some similar issues whilst others different from the brazilian context [56] . while the absence of specific measures to protect those with diabetes was reported in greece and spain, access to medicines was a challenge in zimbabwe, iran and india [56]. however, countries like argentina, italy, portugal, and south korea seemed to have adopted measures that made people with diabetes feel safer [48, 56] . it is urgent for brazil to follow international best practices and recommendations, since, as stated by the who regional office for europe, "the prevention and control of ncds have a crucial role in the covid-19 response and an adaptive response is required to account for the needs of people with ncds" [17] . imitations of the present study, although efforts were made to disseminate the survey as much as possible, this study's sample neither reflects the proportion of brazilian population nor the fraction with diabetes. thus, it is a convenience sample, without post-stratification weights. questions about behaviors, habits and glycemic changes were subjective comparisons with the pre-pandemic state, therefore, we did not have access to objective data to validate the subjective responses. as an online survey, it is biased by individuals who have internet access. while 17% of the brazilian population have a college degree [57] and 27.9% have private health insurance [28] , among the respondents of the present survey, 51.8% had at least one college degree and only 28.2% exclusively access care services through sus. other demographic limitations related to the age groups distribution, younger than the general population with the great majority of the respondents from sao paulo state, which would be about 20% of the country, not 42.6% as in our group of respondents. we understand that one of the main factors leading to this bias is the network in which the authors are engaged, the geographic location of diabetes associations and the profile of their active members, tendency to have more individuals with t1d than t2d, mostly young and highly educated. ann additional limitation is the number of choices for each question and the aggregation made for analysis purposes. this includes the fact that if separated, diseases aggregated in the cardiovascular disease group, for example, could behave differently in terms of proximity to other factors; moreover, increase or decrease of the blood glucose, interpreted as distancing from the target, would in fact have led the glycemic to target, while the ones who successfully maintained the blood glucose in pre-pandemic levels, may have kept it out of target. as revealed for the first time in the current study, individuals with diabetes were not spared by the covid-19 pandemic in brazil. measures and adjustments lacked or were insufficient, paving the way to unhealthy and unsafe behaviors such as postponing medical appointments, reducing physical activity and refraining from collecting medication and supplies, which led to a high percentage of glycemic worsen reports. additionally, announced measures for prevention and mitigation of covid-19 consequences on this population, such as supply of medicines for 3 months, worked just for a minority. in conclusion, we see a pressing need from the brazilian federal, states and municipal authorities to broaden the already implemented measures in order to reach more people, and partner with civil society, private sector and media channels to quickly improve the response and, this way, prevent a surge of individuals with diabetes infected by sars-cov-2 and of acute and chronic diabetes complications. among the priorities measures to keep individuals healthy is by ensuring their glycemia is on target and they are at home as much as possible. we recommend that the public and the private health systems maintain and strengthen programs for the continuity of care of individuals with diabetes and other ncds, and develop information and educational campaigns on how to access those measures. in addition to focusing on reducing the risk of infection and continuity of their healthcare, these measures should facilitate access to healthcare professionals' counseling for therapeutic adjustment. finally, as key measures we foresee are a) activemonitoring and response to communities' needs at primary heathcare level; b) high quality telehealth for consultations to monitoring and examining; c) distribution of medications and supplies for three or more months, ideally with home delivery; d) lab exams scheduled through home sampling, using mobile point-ofcare strategies or appointment in specific facilities with well established disinfection protocols. consequently, we believe that the pandemic's challenges can be lessened if appropriate measures protecting individuals with diabetes and other chronic conditions are adopted, and investments are not solely directed to purchasing mechanical ventilators and equipping tertiary care. epidemiology, public policies and covid-19 pandemics in brazil: what can we expect? revista de enfermagem uerj covid-19 in brazil: advantages of a socialized unified health system and preparation to contain cases. sociedade brasileira de medicina tropical covid-19 in latin america: the implications of the first confirmed case in brazil south america prepares for the impact of covid-19 characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study. the lancet preparación y control de la enfermedad por coronavirus 2019 (covid-19) en américa latina covid-19: towards controlling of a pandemic covid-19 in italy: momentous decisions and many uncertainties who. coronavirus disease (covid-19) pandemic the lancet. covid-19 in brazil report 21: estimating covid-19 cases and reproduction number in brazil pesquisadores estimam haver mais de 1,6 milhão de casos de covid-19 no brasil covid-19 infection in italian people with diabetes:lessons learned for our future (an experience to be used) care for diabetes with covid-19: advice from china prevention and control of noncommunicable diseases in the covid-19 response clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study. the lancet association of blood glucose control and outcomes in patients with covid-19 and pre-existing type 2 diabetes admission hyperglycemia and radiological findings of sars-cov2 in patients with and without diabetes glycemic characteristics and clinical outcomes of covid-19 patients hospitalized in the united states elevated glucose levels favor sars-cov-2 infection and monocyte response through a hif-1α/glycolysis dependent axis hyperglycemia and the worse prognosis of covid-19. why a fast blood glucose control should be mandatory clinical characteristics and risk factors for mortality of covid-19 patients with diabetes in wuhan, china: a two-center international diabetes federation prevalence of diabetes mellitus as determined by glycated hemoglobin in the brazilian adult population, national health survey an analysis and synthesis of multiple correspondence analysis, optimal scaling, dual scaling, homogeneity analysis and other methods for quantifying categorical multivariate data private health care coverage in the brazilian population, according to the 2013 brazilian national health survey. ciência & saúde coletiva paho. if i have diabetes, what do i need to know about covid-19? securing the safety net and protecting health during a pandemic: medicaid's response to covid-19 alterações no programa farmácia popular devido à situação de emergência de saúde pública decorrente do coronavírus (covid19 saúde amplia entrega de remédios nas farmácias de alto custo para prevenção do coronavírus covid-19 and diabetes prevention and management of covid-19 among patients with diabetes: an appraisal of the literature delayed access or provision of care in italy resulting from fear of covid-19 covid-19 and endocrine diseases. a statement from the enfermedad por coronavirus 2019 (covid-19) en américa latina: papel de la atención primaria en la preparación y respuesta public health measures and the reproduction number of sars-cov-2 covid-19 impact on people with diabetes in the south and central america deep impact of covid-19 in the healthcare of latin america: the case of brazil social isolation during the covid-19 pandemic can increase physical inactivity and the global burden of cardiovascular disease risk of increased physical inactivity during covid-19 outbreak in older people: a call for actions managing covid-19 in low-and middle-income countries what is the role of primary health care in the covid-19 pandemic? practical recommendations for the management of diabetes in patients with covid-19. the lancet the silver lining to covid-19: avoiding diabetic ketoacidosis admissions with telehealth coronavirus infections and type 2 diabetes -shared pathways with therapeutic implications ensuring people-centred diabetes care during the covid-19 pandemic experiences from portugal beyond the virus: ensuring continuity of care for people with diabetes during covid-19. primary care diabetes obesity and covid-19 severity in a designated hospital in shenzhen, china. diabetes care covid-19 and diabetes: knowledge in progress type 1 diabetes and covid-19: preliminary findings from a multicenter surveillance study in the u.s. diabetes care critical care utilization for the covid-19 outbreak in lombardy, italy clinical considerations for patients with diabetes in times of covid-19 epidemic world health organization, rapid assessment of service delivery for ncds during the covid-19 pandemic covid-19: perspectives from people with diabetes education at a glance 2019. country note brazil the authors acknowledge vanessa pirolo's support and assistance sharing the survey through her network and the non-governmental organizations adj diabetes brasil (adj), institute for children with diabetes (icd), brazilian diabetes society (sbd), brazilian hypercholesterolemia association (ahf), fórumdcnts and their member and partner entities for assisting in sharing the survey and providing general support. key: cord-351430-bpv7p7zo authors: pequeno, pedro; mendel, bruna; rosa, clarissa; bosholn, mariane; souza, jorge luiz; baccaro, fabricio; barbosa, reinaldo; magnusson, william title: air transportation, population density and temperature predict the spread of covid-19 in brazil date: 2020-06-03 journal: peerj doi: 10.7717/peerj.9322 sha: doc_id: 351430 cord_uid: bpv7p7zo there is evidence that covid-19, the disease caused by the betacoronavirus sars-cov-2, is sensitive to environmental conditions. however, such conditions often correlate with demographic and socioeconomic factors at larger spatial extents, which could confound this inference. we evaluated the effect of meteorological conditions (temperature, solar radiation, air humidity and precipitation) on 292 daily records of cumulative number of confirmed covid-19 cases across the 27 brazilian capital cities during the 1st month of the outbreak, while controlling for an indicator of the number of tests, the number of arriving flights, population density, proportion of elderly people and average income. apart from increasing with time, the number of confirmed cases was mainly related to the number of arriving flights and population density, increasing with both factors. however, after accounting for these effects, the disease was shown to be temperature sensitive: there were more cases in colder cities and days, and cases accumulated faster at lower temperatures. our best estimate indicates that a 1 °c increase in temperature has been associated with a decrease in confirmed cases of 8%. the quality of the data and unknowns limit the analysis, but the study reveals an urgent need to understand more about the environmental sensitivity of the disease to predict demands on health services in different regions and seasons. the disease covid-19, caused by the betacoronavirus sars-cov-2, has caused panic throughout the world by overwhelming medical services in many countries, leading to deaths that might have been avoided if patients had access to intensive-care units (icus). this has led to an unprecedented collaboration within and among countries to slow the spread of the disease, principally using social distancing (ebrahim et al., 2020; wilder-smith & freedman, 2020) . while it is not clear how much present policies will reduce overall infection rates by sars-cov-2, there is consensus that slowing the spread of the disease will save lives by tailoring patient demands to the capacity of health systems walker et al., 2020) . the strategies of social isolation applied in countries on all continents have allowed time for authorities to undertake interventions to strengthen their health systems, and one of the main actions is to estimate the number of cases of covid-19 in each region (anderson et al., 2020; walker et al., 2020) . this information is essential to scale the number of icus to the number of critically ill patients who normally require supportive lung ventilation . brazil has a large per capita number of icus in comparison with europe, but those units are not evenly spread among regions, with more icus per capita in southern states than in northern regions, leaving many brazilians at large distances from the nearest icu (rhodes & moreno, 2012) . moreover, the large demographic and socioeconomic discrepancies in the country create significant variation in susceptibility to infectious diseases (barreto et al., 2011) . one of the problems in predicting the demand for hospital services is that the disease is new so that its behavior is still poorly understood, and the virus may be evolving rapidly (zhao et al., 2004; yang et al., 2020; morais et al., 2020) . therefore, models developed in one country may give poor predictions in another. habitat-specificity modeling suggests that sars-cov-2 spread may be related to environmental conditions, especially temperature and humidity (sajadi et al., 2020; wang et al., 2020) . further, at the host level, there is circumstantial evidence that covid-19 is related to shortage of vitamin d, which could result from limited exposition to solar radiation (grant et al., 2020) . indeed, it has been suggested that solar radiation might deactivate the virus (poole, 2020) . although preliminary, these results provide a plethora of mechanistic processes linking weather and virus spread that need to be better understood. brazil is one of the largest countries in the world, spanning both hemispheres, with latitudes varying from 5 n to 33 s. this means that climatic conditions vary greatly and simple models that do not take into account the possible environmental sensitivity of covid-19 might not be adequate to predict when and where there will be the greatest demand for health services in brazil (fig. 1 ). one difficulty in quantifying this sensitivity is that climate is likely to correlate with demographic and socioeconomic factors across larger spatial extents. thus, environmental effects could be confounded unless risk factors for viral spread are taken into account, such as population density, transport connectivity and economic status (poole, 2020; wang et al., 2020; ribeiro et al., 2020) . in an attempt to determine whether environmental variables have significant effects on the propagation of covid-19, we modeled the daily cumulative number of confirmed cases among brazilian capital cities in relation to meteorological variables during the 1st month of the disease in the country, while controlling for several demographic and socioeconomic factors. we used only capital cities because they are presently the only reliable sources of covid-19 cases and represent much of the climatic variation within brazil. data on connectivity and frequency of cases is not presently adequate to model the spread of the disease at the municipal level, but this should be available in the future and can be used to test our hypotheses. we obtained daily cumulative counts of confirmed cases of covid-19 for each of the 27 brazilian state capital cities, as reported by state health secretaries and compiled by volunteers (table s1 ; secretarias de saúde das unidades federativas, 2020). march, 2020 (n = 27); (secretarias de saúde das unidades federativas, 2020), superimposed on the country's thermal variability. temperature data represent means for march over 1989-2019 (fick & hijmans, 2017) , and were used only in the map; actual analyses used current, daily meteorological data. full-size  doi: 10.7717/peerj.9322/ fig-1 we focused on the month since the first confirmed case, from february 26 to march 26, 2020, for which there were 292 reports on daily counts across cities. we considered several potential predictors of the number of confirmed cases. first, it was important to account for the number of tests for covid-19, as performing more tests tends to reveal more positive cases (roser et al., 2020) . the brazilian government has not been systematically reporting the number of performed tests, but has recommended testing of all suspected patients with severe symptoms, and the ministry of health reported the number of suspected cases per state until march 18, 2020. therefore, we used the number of suspected cases per state on that date as a proxy for the number of tests, under the reasonable assumption that states with more suspected cases performed more tests. further, we considered the following predictors: (1) time in days, to account for the exponential growth in case numbers during this period (fig. 2) ; (2) number of arriving flights in the city's metropolitan area in 2020, as airline connections can facilitate the spread of the virus (ribeiro et al., 2020) ; (3) city population density, to account for facilitation of transmission under higher densities (poole, 2020) ; (4) proportion of elderly people (≥60 years old) in the population, assuming that the elderly may be more likely to show severe symptoms of sars-cov-2 and, thus, to be diagnosed with covid-19; (5) citizen mean income, which may affect the likelihood of people being infected by the virus, for example, due to limited access to basic sanitation or limited social isolation capabilities; (6) and the following meteorological variables: mean daily temperature ( c), mean daily solar radiation (kj/m 2 ), mean daily relative humidity (%) and mean daily precipitation (mm). the number of suspected cases and socioeconomic variables only varied across cities, whereas meteorological variables varied both between and within cities. data on population density, the elderly and income were obtained for the last quarter of 2019 from the brazilian institute for geography and statistics (ibge), which samples brazilian households quarterly for socioeconomic indicators (sidra, 2020) (table s2) . flight data were obtained from the current statistical annuary of the brazilian agency for civilian aviation (anac) ( table s3 ; anac, 2020). hourly meteorological data were obtained from the automatic stations maintained by the brazilian institute for meteorology (inmet) in the capital cities (table s4 ; inmet, 2020). we investigated the response of case counts to putative predictors using a generalized linear mixed model (glmm) assuming poisson-distributed errors and log link, and using capital-city identity as a random factor to account for autocorrelated errors within cities. this formulation induces a compound symmetry correlation structure on residuals within cities, which is mathematically equivalent to that of classical, "repeated measures" linear models (zuur et al., 2009) . the numbers of suspected cases and arriving flights were log-transformed to account for their highly skewed distributions, and all predictors were scaled to zero mean and unit standard deviation to facilitate parameter estimation. consequently, estimated coefficients were scaled, thus providing a measure of predictor relative importance. specifically, assuming a log link, a change of one unit in the scaled predictor implies a mean percent change of (exp(coefficient/sd) − 1) × 100 in the number of confirmed cases, where "coefficient" and "sd" are the predictor's model coefficient and standard deviation, respectively. we considered time lags in the effect of meteorological conditions. incubation time of covid-19 averages 5 days (lauer et al., 2020) , and case confirmation in brazil has taken from several days to 2 weeks due to overload of test laboratories. therefore, the time between infection and case confirmation is likely to be longer than a week. accordingly, we considered a set of models including all predictors but varying in the number of days meteorological predictors were lagged relative to case counts, ranging from 7 to 30 days with daily steps. then, models were compared with akaike's information criterion (aic), a standard measure of model relative support, and the model with the lowest aic was judged as the most supported. precipitation time series had missing intervals for some capital cities. therefore, we performed two versions of the above analysis: one including all predictors but excluding days for which precipitation was lacking (n = 269) and another one excluding precipitation as predictor and using all counts of confirmed covid-19 cases (n = 292). because both analyses produced largely similar results, with precipitation having a negligible model coefficient (figs. s1 and s2; table s5 ), we present the analysis using the larger sample. lastly, we considered possible interactions between time and other predictors, assuming some factors could accelerate the temporal increase in number of confirmed cases. by definition, glmms assuming a log link implicitly account for interactive effects to some degree, as log-linear models imply multiplicative effects. still, we ran a separate glmm which explicitly included interaction terms between time and the remaining predictors. to avoid model overparameterization, we only used the significant predictors identified in the previous analysis. for all models, we computed the conditional predictive power (r 2 c ), which indicates the variance explained jointly by predictors and the random factor, and the marginal predictive power (r 2 m ), which only considers predictor effects. in these calculations, only significant predictors were retained in the model to avoid inflation of explained variance due to spurious parameters. we acknowledge that it would be better to directly model the spread of sars-cov-2, but we cannot do that without making assumptions about the relationship between infection by the virus and the appearance of symptoms of the disease, which may be related to the factors that we are investigating. all analyses were performed in r 3.6.3 (r core team, 2020), with aid of packages "coronabr" (mortara, sánchez-tapia & martins, 2020) and "covid19br" (paterno, 2020) for assessing counts of suspected cases by state, "lme4" for glmm (bates et al., 2015) , "mumin" for aic and r² calculations (barto n, 2019), and "visreg" for visualization of predictor effects (breheny & burchett, 2017) . there was strong support for the model whose meteorological predictors were lagged by 15 days, as indicated by its much lower aic (fig. 3) . according to this model, the only significant predictors of the number of confirmed covid-19 cases were time, the number of arriving flights, population density and temperature (table 1 ). the number of confirmed cases increased with time (fig. 4a ), the number of arriving flights (fig. 4b ) and population density (fig. 4c) , whereas it decreased with temperature (fig. 4d ). considering that model coefficients were scaled, comparing their values gives an indication of the relative importance of each predictor. accordingly, time, the number of arriving flights and population density had the strongest effects (i.e., largest coefficients), followed by temperature (table 1) . nevertheless, a change in 1 c predicted a decrease in the number of confirmed cases by (exp(−0.26/3.11) − 1) × 100 = 8%, independently of other factors (table 1 ). significant predictors explained 77% of the variance of daily counts of confirmed covid-19 across capital cities in brazil. explicitly accounting for interactions between time and the remaining predictors identified in the previous analysis suggested significant interactions between time and the number of arriving flights, and time and temperature, although the magnitude of the interaction coefficients was low (table 2) . on average, the temporal increase in confirmed covid-19 cases began earlier in cities with more flights, causing a leftward shift in the relationship between confirmed cases and time (fig. 5a ). in parallel, the number of confirmed cases increased faster at lower temperatures, causing a steeper slope in the relationship between confirmed cases and time (fig. 5b) . however, these effects were relatively weak, and there was no improvement in predictive power (table 2) . thus, the previous, simpler model captured the main patterns in the data very well. table 1 results of the most supported generalized linear mixed model (glmm) testing for independent effects on daily cumulative counts of confirmed covid-19 across the 27 capital cities in brazil (n = 292; r 2 c = 0.98; r 2 m = 0.77). the model assumed poisson-distributed errors and log link, and used capital city identity as a random factor to account for autocorrelated errors of time series within cities. all predictors were scaled to zero mean and unit standard deviation. sd indicates predictor standard deviation; numbers in bold represent statistically significant effects (p < 0.05). variables were as follows: time-time elapsed in days; log suspected-log-transformed number of suspected covid-19 cases in march 18, 2020; log flights-log-transformed number of arriving flights in 2020; density-inhabitants by km 2 ; elderly-proportion of elderly people (≥ 60 years old); income-mean citizen income (r$); temperature-mean daily temperature ( c) with a 15-day lag; radiation-mean daily solar radiation (kj/m 2 ) with a 15-day lag; humidity-mean daily air humidity (%) with a 15-day lag. sd coefficient z p our results indicate that the number of confirmed covid-19 cases in brazil has been higher and has begun to increase earlier in cities receiving more flights, consistent with the expected role of air-transport connections in spreading the virus across the country (ribeiro et al., 2020) . further, there have been more cases in cities with higher population density, consistent with the expected role of host density (poole, 2020) . we also have uncovered a temperature response with a lag of 15 days: there have been more confirmed cases in colder cities and days, and confirmed cases have accumulated faster under lower temperature days. although correlative, these patterns were independent of several demographic and socioeconomic factors and, thus, are unlikely to be confounded by them. this is disturbing because there is little that authorities can do about this relationship, log number of confirmed covid−19 cases (partial residuals) table 2 . the model assumed poisson-distributed errors and log link, and included capital city identity as a random factor to account for autocorrelated errors in time series within cities. each point represents a daily observation in a given city (n = 292); lines represent predicted means for each group of observations, as indicated by legends. group medians were chosen based on their respective predictor ranges (see fig. 4 ). plots use partial residuals of the response variable and thus show the effect of a given interaction while controlling the effects of remaining predictors. full-size  doi: 10.7717/peerj.9322/fig-5 table 2 results of the generalized linear mixed model (glmm) testing for interaction effects on daily cumulative counts of confirmed covid-19 in brazil (n = 292; r 2 c = 0.98; r 2 m = 0.77). the model assumed poisson-distributed errors and log link, and used capital city identity as a random factor to account for autocorrelated errors of time series within cities. only statistically significant predictors in table 1 were used, all of which were scaled to zero mean and unit standard deviation. sd indicates predictor standard deviation; numbers in bold represent statistically significant effects (p < 0.05). variables were as follows: time-time elapsed in days; log flights-log-transformed number of arriving flights in 2020; density-inhabitants by km 2 ; temperature-mean daily temperature ( c) with a 15-day lag. whereas the number of arriving flights and population density can be manipulated indirectly by isolation strategies. the temperature dependance of covid-19 in brazil agrees with data from china, where warmer weather also seemed to limit the spread of covid-19 while controlling for population density and per capita gdp . it also agrees with the thermal dependance of viability and transmission demonstrated experimentally for better-studied viruses, such as influenza (lowen et al., 2007) and other betacoronaviruses, for example, sars-cov-1 (chan et al., 2011) and mers-cov (van doremalen, bushmaker & munster, 2013) . while the precise mechanism underlying this pattern requires further study, it may be related to the lipid bilayer of coronaviruses, which becomes increasingly unstable as temperature increases (schoeman & fielding, 2019) . recognizing that we are talking about the rate of spread and not necessarily final mortality rates, the information is still important for authorities trying to predict demands on health services. our best estimate is that a rise of about 1 c in mean daily temperature reduces the number of covid-19 cases by about 8%, independently of other factors. thus, for instance, our results indicate that cuiabá, with a mean july temperature of about 23.4 c, and porto alegre, with a mean july temperature of 14.9 c, may differ up to 50% in the number of covid-19 cases, all else being equal. it also means that the spread in porto alegre might be 41% lower in the middle of march (mean daily temperature of 21.3 c) than it will be in the middle of july (mean daily temperature of 14.9). at the same time, and contrary to some suggestions (poole, 2020; wang et al., 2020; grant et al., 2020) , we found no evidence for effects of solar radiation or humidity. perhaps such conditions are not limiting for the virus or the disease under the climatic conditions of brazil. also, rapid evolution of the climatic niche of sar-cov-2 could have a similar effect. although the mutation rate of sars-cov seems to be moderate compared to that of other rna viruses (zhao et al., 2004; yang et al., 2020) , clustering of hundreds of worldwide sars-cov-2 genomes based on widely shared polymorphisms suggests 16 subtypes, all of which harbor amino acid replacements which may have phenotypic effects (morais et al., 2020) . whether the temperature effect is related to the rate of spread of sars-cov-2 or to the proportion of persons that suffer reportable symptoms cannot be answered with the data being provided at the moment (fasina, 2020) . that would require universal testing for the presence of the virus, which is not presently viable but may be a necessity in the following months. also, one of the main difficulties we encountered was the lack of systematization of current information, since much of the data generated daily is still scattered and difficult to access. for instance, the number of tests performed, which is the key to estimate the rate of infection and the number of infected patients is not available. the large number of publications on the subject in the last 30 days shows that the scientific community is prepared for a quick response, as long as there is a systematization and transparency of information regarding the number of tests being performed, number of suspected cases, number of infected, number of deaths, etc. our models are necessarily simple and have limitations. most importantly, we need city and state administrations to provide the number of performed tests on a regular basis, so that this variable can be explicitly accounted for in the model. the data do not allow us to investigate complex nonlinear effects, which likely would require data on temperatures beyond those observed in brazilian cities in march. also, it is currently not possible to account for potential interactions between covid-19 and other diseases, particularly influenza, which is seasonal. it may not be necessary to worry about this in the northern hemisphere because the peaks in covid-19 will occur after the peaks in seasonal influenza. however, the predicted peaks in covid-19 in the southern hemisphere will occur concomitantly with peaks in seasonal influenza (nelson et al., 2006; viboud, alonso & simonsen, 2006) . the effects may just be additive, but it is not known whether the simultaneous infection will increase the severity of covid-19 and therefore the demand for icus, and this interaction also could be temperature sensitive. further, air pollution is known to increase susceptibility to viral respiratory infections (ciencewicki & jaspers, 2007) , but the extent to which it affects the prevalence of covid-19 is unclear. as covid-19 consolidates in different cities, it will be possible to reduce uncertainties in relation to the role of temperature and other factors. nonetheless, our models still performed well as judged by their predictive power, even when ignoring interactions between predictors. we stress that the temperature effect does not mean that the northern, warmer regions of brazil should expect fewer complications in their health care system, because such regions also have poorer socioeconomic and sanitary conditions (barreto et al., 2011) , and icus are concentrated in southern regions (rhodes & moreno, 2012) . although we found no evidence for an effect of income on the number of confirmed covid-19 cases, this variable is related to the capacity of cities to respond to the pandemic. furthermore, apart from elapsed time, the predictors with the largest standardized coefficients were the number of arriving flights and population density (table 1) . indeed, manaus, the largest city in northern brazil, was the first brazilian city to declare the collapse of the health system early in april 2020, which is consistent with its large number of arriving flights and large population density but relatively low number of icus (rhodes & moreno, 2012) . by contrast, although southern, colder regions have a higher density of icus, their situation could be aggravated if social isolation measures are not effectively adopted before and maintained throughout winter in those regions (from june to september). this should be especially important for "favelas", that is, poorer, highly populated neighborhoods with deficient infrastructure, which are presumably at high risk of infection. thus, we do not present our results as an indication of how hospital demand should be calculated, but as a warning that models for brazil need to take into account predicted temperatures. declared as a pandemic by the world health organization (who), the covid-19 disease has changed human behavior and strongly affected health systems and the economy worldwide. in an extremely demanding scenario, optimizing the distribution of resources is an essential task. brazil and other countries are starting to discuss the flexibilization of social distancing policies, as the latter could have important economic costs. however, we need to understand how and when to implement such decisions in order to prevent new, uncontrolled disease outbreaks that may overcrowd the health care system again and generate even higher economic costs in the near future. our results suggest that, along with arriving flights and population density, temperature should be taken into account to estimate the number of cases of covid-19, especially with winter approaching in the southern hemisphere. agência nacional de aviação civil how will country-based mitigation measures influence the course of the covid-19 epidemic? successes and failures in the control of infectious diseases in brazil: social and environmental context, policies, interventions, and research needs mumin: multi-model inference. r package version 1.43.17 fitting linear mixed-effects models using lme4 visualization of regression models using visreg the effects of temperature and relative humidity on the viability of the sars coronavirus air pollution and respiratory viral infection covid-19 and community mitigation strategies in a pandemic novel coronavirus (2019-ncov) update: what we know and what is unknown impact of non-pharmaceutical interventions (npis) to reduce covid-19 mortality and healthcare demand worldclim 2: new 1-km spatial resolution climate surfaces for global land areas evidence that vitamin d supplementation could reduce risk of influenza and covid-19 infections and deaths the incubation period of coronavirus disease 2019 (covid-19) from publicly reported confirmed cases: estimation and application influenza virus transmission is dependent on relative humidity and temperature the global population of sars-cov-2 is composed of six major subtypes coronabr: download de dados do coronavírus stochastic processes are key determinants of short-term evolution in influenza a virus covid19br: an r-package with updated data on the number of coronavirus (covid-19) cases in brazil seasonal influences on the spread of sars-cov-2 (covid19), causality, and forecastabililty r: a language and environment for statistical computing. vienna: r foundation for statistical computing severe airport sanitarian control could slow down the spreading of covid-19 pandemics in brazil intensive care provision: a global problem coronavirus disease (covid-19)-statistics and research temperature, humidity, and latitude analysis to predict potential spread and seasonality for covid-19 coronavirus envelope protein: current knowledge dados diários mais recentes do coronavírus por município brasileiro pesquisa nacional por amostra de domicílios contínua trimestral: tabela 5918-população por grupo de idade stability of middle east respiratory syndrome coronavirus (mers-cov) under different environmental conditions influenza in tropical regions the global impact of covid-19 and strategies for mitigation and suppression high temperature and high humidity reduce the transmission of covid-19 isolation, quarantine, social distancing and community containment: pivotal role for old-style public health measures in the novel coronavirus (2019-ncov) outbreak pathological findings of covid-19 associated with acute respiratory distress syndrome the deadly coronaviruses: the 2003 sars pandemic and the 2020 novel coronavirus epidemic in china moderate mutation rate in the sars coronavirus genome and its implications mixed effects models and extensions in ecology with r we are grateful to álvaro justen and his collaborators for compiling the daily records on covid-19 cases for brazilian cities, and sara mortara, andrea sánchez-tapia, karlo martins and gustavo paterno for developing r packages to facilitate obtention of covid-19 data from the brazilian ministry of health. we thank the biodiversity research program (ppbio brasil) of the ministry of science, technology, innovation and communication (mctic) of brazil for providing the contact network that enabled quick collaboration among the researchers involved in this manuscript. we also thank alexandre almeida, daniel pimenta and lucas bandeira for useful suggestions on preliminary analyses, and elizabeth franklin, daniela bôlla, fabíola wieckert, sérvio ribeiro and two anonymous reviewers for useful comments on earlier versions of this manuscript. the following grant information was disclosed by the authors: ministry of science, technology, innovation and communication (mctic). cnpq. pedro pequeno conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft. bruna mendel conceived and designed the experiments, performed the experiments, authored or reviewed drafts of the paper, and approved the final draft. clarissa rosa conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft. mariane bosholn conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft. jorge luiz souza conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft. fabricio baccaro conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft. reinaldo barbosa conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft. william magnusson conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft. the following information was supplied regarding data availability:the raw measurements are available in the supplemental files. supplemental information for this article can be found online at http://dx.doi.org/10.7717/ peerj.9322#supplemental-information. the authors declare that they have no competing interests. key: cord-287911-aoulao8w authors: hone, thomas; powell-jackson, timothy; santos, leonor maria pacheco; de sousa soares, ricardo; de oliveira, felipe proenço; sanchez, mauro niskier; harris, matthew; de oliveira de souza santos, felipe; millett, christopher title: impact of the programa mais médicos (more doctors programme) on primary care doctor supply and amenable mortality: quasi-experimental study of 5565 brazilian municipalities date: 2020-09-15 journal: bmc health serv res doi: 10.1186/s12913-020-05716-2 sha: doc_id: 287911 cord_uid: aoulao8w background: investing in human resources for health (hrh) is vital for achieving universal health care and the sustainable development goals. the programa mais médicos (pmm) (more doctors programme) provided 17,000 doctors, predominantly from cuba, to work in brazilian primary care. this study assesses whether pmm doctor allocation to municipalities was consistent with programme criteria and associated impacts on amenable mortality. methods: difference-in-differences regression analysis, exploiting variation in pmm introduction across 5565 municipalities over the period 2008–2017, was employed to examine programme impacts on doctor density and mortality amenable to healthcare. heterogeneity in effects was explored with respect to doctor allocation criteria and municipal doctor density prior to pmm introduction. results: after starting in 2013, pmm was associated with an increase in pmm-contracted primary care doctors of 15.1 per 100,000 population. however, largescale substitution of existing primary care doctors resulting in a net increase of only 5.7 per 100,000. increases in both pmm and total primary care doctors were lower in priority municipalities due to lower allocation of pmm doctors and greater substitution effects. the pmm led to amenable mortality reductions of − 1.06 per 100,000 (95%ci: − 1.78 to − 0.34) annually – with greater benefits in municipalities prioritised for doctor allocation and where doctor density was low before programme implementation. conclusions: pmm potential health benefits were undermined due to widespread allocation of doctors to non-priority areas and local substitution effects. policies seeking to strengthen hrh should develop and implement needs-based criteria for resource allocation. investments in human resources for health (hrh) which deliver sufficient numbers of highly-skilled, motivated and equitably distributed health professionals [1] are essential to achieve universal health care and health targets in the sustainable development goals (sdgs). however, chronic hrh shortages persist in many settings with an estimated 10.3 million extra health workers needed globally to achieve uhc [2] . interventions to address hrh deficiencies are essential, but so is ensuring implementation as planned to achieve their intended benefits. brazil, like many other low-and middle-income countries (lmics), suffers substantial hrh challenges. supply of doctors is low by international standards (180 per 100,000 population in 2013 [3] ) with large geographic distributional inequalities. many doctors work in the private hospital sector in urban areas rather than the public system where working conditions and career prospects are perceived to be poor [4, 5] . in 2012, over 42% of the population lived in areas with fewer than 25 doctors per 100,000 [6] comparable to doctor densities in countries of sub-saharan africa (20 per 100,000) [7] . hrh shortages in primary care are especially problematic and contribute to suboptimal health outcomes and continued health inequalities in the country [8] . brazil's estratégia saúde da família (esf) is a globally-renowned public primary care system that has delivered improvements in health outcomes [9] [10] [11] [12] [13] . however, expansion of the esf in urban or remote areas has stalled in recent years due to hrh shortages [14] . in 2013, the brazil government initiated the programa mais médicos (pmm) (more doctors programme) to expand the number of doctors in under-served areas. in addition to funds for clinic construction and refurbishment, and new medical schools in areas lacking doctors, there was a politically-contentious "emergency expansion" of primary care doctors. these were predominantly cuban doctors who entered brazil following an agreement between cuba and brazil, organised by the pan american health organisation (paho). one year later, in july 2014, there were 14,462 pmm doctors: 79.0% cubans (11, 429) , 15 .9% brazilians (2302) and 5.1% other foreigners (731) [15] . by sept 2015, the total had increased to 17,625 doctors [3] . studies show that following the pmm there are now fewer municipalities with primary care doctor shortages [16, 17] , access to doctors has increased, users are more satisfied, and services have improved including patient-doctor relations, continuity, and coordination [18, 19] . there is also evidence of reductions in hospitalisations, but no effect on infant mortality [20, 21] . however, little is known about pmm's impact on existing primary care services or adult mortality. primary care expansion in brazil led to reductions in child and amenable adult mortality [10] , health inequalities [11] , and ambulatory care sensitive hospitalisations [9] , and therefore health improvements from pmm are anticipated. criteria for allocating pmm doctors to brazil's 5565 municipalities were developed prior to programme implementation, and based on indicators of local deprivation rather than a formal health needs assessment [22] . actual allocation was widespread with 4509 (81.0%) municipalities receiving pmm doctors, including municipalities already achieving international benchmarks for doctor supply. pmm implementation provides important policy learning opportunity about prioritising scarce hrh to maximise health system performance and health outcomes [23] . this study examined the impact of pmm on primary care doctor supply and amenable mortality using longitudinal data from 5565 brazilian municipalities between 2008 and 2017. it explored whether these relationships differ in areas prioritised under pmm allocation criteria, compared with those that were not, and by primary care doctor density prior to pmm introduction. the brazilian government launched programa mais médicos (pmm) in july 2013 with three main componentsan "emergency" expansion of primary care doctors, establishing new medical schools with increases in primary care residency positions, and funds for clinic construction and refurbishment. the "emergency" expansion was the most visible and politically contentious component of pmm. initially, local managers requested 16,000 primary care doctors to fill vacancies in underserved areas. competitive salaries were offered under pmm to encourage brazilian doctors to relocate, but only 1096 brazilian doctors enrolled [15] . an international cooperation agreement between brazil and cuba facilitated by paho provided cuban doctors to fill these vacancies following basic training in primary care and supervision from an accredited university [3, 24] . municipalities were prioritized to receive pmm doctors using federally-set criteria: municipalities with 20% or more of the population in extreme poverty; 100 municipalities with more than 80,000 population and the lowest income per capita; state capitals, metropolitan regions, and other municipalities encompassing areas with extreme poverty; and municipalities with low/ very low human development index or considered vulnerable (e.g. semi-arid or quilombo communities) [6] . however many non-priority municipalities received pmm doctors [6] as the brazilian ministry of health did not adhere to these criteria. the costs of the pmm were substantial. in 2014, medical provision costs were us$ 1.1 billion (r$ 2.36 billion), 93% financed by the federal budget, or approximately us$ 6000 (r$ 14,000) per month per doctor [25] . funding for clinic construction and refurbishment exceeded r$5 billion [3] . by 2019, 13,000 new undergraduate medical places had also been created. however, construction and refurbishment of clinics and establishment of new medical schools was paused following a federal funding freeze. in november 2018, the cuban government withdrew all cuban doctors from brazil citing critical comments by president-elect jair bolsonaro. during the election period, he questioned the quality of their training and described them as "slaves" due to the low pay they receive (relative to payments made to the cuban government) [5] . in august 2019 the government launched a new program called "medicos pelo brasil" (doctors for brazil), but as of november 2019, approximately 5000 positions remain vacant. this study employed differences in differences approaches using longitudinal (panel) regression models to compare the supply of primary care doctors and mortality amenable to healthcare before and after pmm introduction between municipalities that received the programme and municipalities that did not. it uses a panel dataset of 5565 brazilian municipalities over the period 2008-2017. longitudinal (panel) regression models are widely employed for programme evaluations [26] and exploit the varied roll out of the pmm programme over time across brazilian municipalities. multiple publicly available data sources were collated. official statistics on mortality, doctors, hospital beds, private health insurance plans, and municipal health expenditures were collated from the brazilian ministry of health website. data on pmm implementation was obtained from the brazilian ministry of health including the number and nationality of pmm doctors in each municipality. the website of the brazilian national institute of geography and statistics (instituto brasileiro de geografia e estatistica -ibge) was consulted for municipal-level data on population, gross domestic product (gdp), bolsa familia expenditure, and sociodemographic characteristics. the main outcome variables of interest were public primary care doctor density per 100,000 (defined as doctors working in public primary care) and mortality amenable to healthcare (per 100,000 population)both expressed at the municipal level. quarterly data on doctor numbers in a municipality and their employment hours were used to generate full time equivalents (ftes) based on a 40-h working week. primary care doctors were identified as those reporting ambulatory working hours in primary care facilities (health centres and posts, family health units, mixed healthcare units, water-based clinics serving fluvial communities, and indigenous health centres). public primary care doctor density was further subdivided into pmm and non-pmm doctorsidentified by their contract with the ministry of health. a variable denoting the percentage of pmm doctors that were brazilian was generated for each quartermunicipality observation. amenable mortality rates were generated from official death statistics which were encoded based on reported icd10 codes and age [27] an approach employed previously [10] . additionally, groups of amenable deaths were encoded based on categories of causes (see additional file 1). annual municipal population estimates were interpolated to generate quarterly observations and, using the age distribution of the population for each municipality from the latest census, denominator populations under 75 years of age were estimated. a binary variable indicating the presence of pmm in a municipality was our exposure variable. it was defined as any pmm doctor operating in a municipality for each quarter-year to account for the time-varying nature of implementation in each municipality and that pmm doctors could leave municipalities. differences-in-differences analyses were employed with multiple time points using longitudinal fixed effects regression models. these models were used to identify associations between pmm introduction and changes in outcomes over time by comparing changes in mortality rates between areas that received the pmm and those that did not before and after pmm implementation. existing studies examining hospitalisations and healthcare utilisation have employed similar analytical strategies and demonstrate the appropriateness of these approaches and validity of underlying assumptions [20, 21, 28, 29] . the regression models adjust for municipality fixed effects (rather than random effects specification) to control for time-invariant differences between municipalities. they further adjusted for state-quarter-year fixed effects and time-varying municipality characteristics. timevarying confounders were chosen as proxies of socioeconomic and demographic characteristics of municipalities and to capture wider changes in the health system as used in similar studies [10, 11, [30] [31] [32] . specifically there were: municipal health expenditure (r$) per capita; private insurance plan coverage (%); hospital bed density (beds per 1000 population); municipal gross domestic production (gdp) per capita (r$); bolsa familia expenditure per poor person (r$), municipal illiteracy rate (%) (of those aged 15 years or more); percentage households with inadequate sanitation (%); municipal urbanisation rate (%); average municipal income per capita (r$); and percentage households with no electricity (%). firstly, trends were explored descriptively and the effect of pmm implementation on doctor density and amenable mortality modelled using longitudinal fixed effects regression models. models exploring mortality were weighted by average municipal population over the period to provide estimates relevant to an average individual (rather than an average municipality). robust standard errors (clustered by municipality) were used to account for heteroskedasticity and autocorrelation [33] . data was analysed using quarterly observations, but effect sizes for mortality were reported as annual to aid interpretability. secondly, heterogeneity in pmm impact was assessed by allocation criteria and baseline primary care doctor density. municipalities were grouped into either priority or non-priority based on allocation criteria. a priority municipality was one that met any of the criteria. municipalities were also divided into five equal sized groups (quintiles) based on the mean density of primary care doctors (fte primary care doctors per 100,000 population) in the period prior to pmm implementation (2008) (2009) (2010) (2011) (2012) . interactions with the indicator of pmm introduction were used to explore subgroup differences in separate models for programmatic priority and baseline doctor density quintiles. to aid interpretation, the reported effect sizes are calculated as the effect of pmm introduction in each group or quintile (rather than marginal effect sizes relative to q1 as commonly reported). thirdly, heterogeneity between brazilian pmm and foreign pmm doctors was assessed to explore whether differential pmm impacts existed by the percentage of pmm doctors that were foreign. a categorical variable was created denoting the combination of pmm implementation and percentage of pmm doctors that were brazilian. specifically: no pmm implementation; < 20% pmm doctors brazilian; 20-80% pmm doctors brazilian; and > 80% pmm doctors brazilian. this variable was used in the main regression model described above. model specifications with variations in time and fixed effects were tested. these included additional statequarter-year fixed effects and state-year-quarter linear time trends. univariate analyses and stepwise addition of covariates were undertaken to explore stability of effect estimates and the models. in addition to step changes following pmm introduction, slope changes (in underlying trends) were also tested. the provab programme (program to value primary healthcare professionals; programa de valorização do profissional da atenção básica) was operational at a similar time to the pmm. it offered training for primary care doctors which was incorporated into the pmm in 2016 (allowing these doctors to also enter the pmm). possible bias from cointroduction of this programme was tested by repeating regression analyses with provab-pmm doctors omitted. models with alternative covariate specifications, including linear time trends interacted with baseline covariate values (2008 q1) were used to assess the robustness of the findings. additionally, inverse probability weighting of treatment (iptw) was employed to test whether further weighting of municipalities by baseline covariates would affect regression results. an event study analysis was also carried out on doctor density outcomes and amenable mortality to examine evidence of pre-trends and test robustness of the findings to alternative analytical approaches. total fte doctors in brazil increased from 268,970 in q1 2008 to 418,566 in q4 2017 representing an increase from 145.1 to 210.6 per 100,000 population (see additional file 1). however, the proportion working in the public sector decreased (from 86.8 to 75.3%). total fulltime equivalent (fte) doctors working in primary care in the public system (hereafter 'primary care doctors') grew 14.2% from 60,900 to 69,536. although, as the number of doctors in other parts of the public system increased, the proportion of primary care doctors declined (from 26.1 to 22.1%) (fig. 1) . over the period 2013-2017, 35,060 pmm doctors were contracted -72.8% of these were non-brazilian. the peak number of pmm doctors working was in q1 2016 with 18,088 doctors in operation. of 5565 municipalities, 4509 (81.0%) ever received a pmm doctor between 2013 and 2017, but this averaged 4000 municipalities from mid-2015 onwards (see additional file 1). this compares to the 46.5% (2589) of municipalities prioritised for pmm allocation under programme criteria; including 1527 due to high levels of extreme poverty, 486 capitals or in metropolitan areas, 98 classified as populations over 80,000 and low incomes, and 478 under other vulnerabilities (semi-arid, low human development index, indigenous areas). pmm introduction coincided with increases in total primary care doctors, but there were concurrent reductions in the number of non-pmm primary care doctors. the mean number of municipal primary care doctors (ftes) per 100,000 grew 11.0% from 46.1 in q1 2012 to 51.6 in q4 2017. regions with lowest primary care density at baseline were mainly in the north and north east of brazil and were also the areas that had the largest increases in doctor density following pmm introduction (fig. 2) . in adjusted differences-in-differences models, pmm introduction was associated with an increase of 5.7 (95%ci, 5.1, 6.4) total primary care doctors per 100, 000 (table 1) (table 1 ). there was no indication of ongoing reductions (slope change) in amenable mortality following pmm introduction over above annual trends (see additional file 1). with an average annual amenable mortality rate of 83.6 deaths per 100,000 over the period, this corresponds to a 1.3% reduction. this effect was predominantly driven by reductions in respiratory diseases including influenza and pneumonia (see additional file 1). exploring heterogeneity of impact by municipality prioritisation for pmm (table 2 ) revealed larger increases in primary care doctor density following pmm introduction in non-priority (7.43 doctors per 100,000 (95%ci, 6.49, 8.36, 14% relative increase) than priority municipalities (4.32 (95%ci, 3.65, 4.99); 10% relative increase). this was driven by greater allocation of pmm doctors to non-priority municipalities and higher rates of substitution of non-pmm doctors in priority municipalities. notably, pmm introduction was associated with reductions in amenable mortality in priority municipalities (− 1.26 (95%ci, − 2.08, − 0.44), but not in nonpriority municipalities. the pmm was associated with larger increases in total primary care doctor density in municipalities that had lower densities of primary care doctors at baseline compared to municipalities with higher baseline doctor density (table 2 ). however, this overall increase in total doctors was driven by two opposing trends. municipalities with higher doctor density at baseline experienced larger increases in pmm doctors following pmm implementation, but also increases in substitution of existing doctors. thus, q5 (highest baseline doctor density) received the greatest increase in pmm doctors, but there was near complete substitution of non-pmm doctors and no significant change in overall primary care doctor density following pmm introduction. this compared to municipalities in q1 (lowest) which had lower increases in pmm density, but the lowest rates of substitution resulting in the largest increases in overall primary care doctor density. notably, there were reductions in mortality associated with pmm introduction in municipalities q1, q2, and q3 (lower baseline doctor density), differential associations of the pmm by pmm doctor nationality were examined. total primary care doctor density increased the most in municipalities where pmm doctors were mostly foreign (i.e. non-brazilian) ( table 3 ). whilst these areas had higher increases in pmm doctors, and also higher rates of substitution of non-pmm doctors, they were the only areas where there were reductions in amenable mortality associated with pmm introduction (− 1.50 deaths per 100,000 per year (95%ci,-2.32,-0.69). models were robust to alternative time and state fixed effects specifications (see additional file 1). stepwise addition of covariates indicated the stability of the modelling approach. the provab programme only contributed a small proportion of doctors entering the pmm (1544 ftes in q4 2015, 9.0% of the total pmm ftes). adjusting the pmm analysis to remove these doctors did not alter the main findings and effect sizes. alternative specifications of covariates including interactions of linear time trends with baseline covariates did not substantially alter our findings. furthermore, the use of iptw revealed similar findings with pmm introduction associated with a lower amenable mortality rate of − 1.61 deaths per 100,000 (95%ci, − 2.72 to − 0.49) per year. event study approaches demonstrated the validity of the analytical approach and confirmed the main findings. this study found the pmm in brazil led to increases in primary care doctor density and was associated modest (1.4%) reductions in mortality amenable to healthcare. however, several findings indicate that programme impacts were lower than might be anticipated. the original criteria for prioritising municipalities to receive pmm doctors was not adhered to (81.0% of municipalities received a pmm doctor but only 46.5% met criteria), and there was large-scale substitution of existing primary care doctors. as a result, municipalities prioritised under programme criteria received fewer pmm doctors than non-priority municipalities where substitution effects were greater. likewise, municipalities with a greater need for doctors received the smallest increases in pmm doctors. allocation of doctors to non-priority areas and local substitution effects likely undermined potential health benefits of pmm. any municipality requesting a pmm doctor received at least one doctor. the substitution of existing doctors, particularly in areas with the greater primary care doctors at baseline, may be explained by a few factors. although formal substitution was not allowed, more stringent attendance, training and supervision requirements for pmm doctors (particularly the cubans) may have prompted existing doctors with high rates of absenteeism to leave [34] . additionally, existing brazilian doctors may have joined pmm due to higher remuneration and reliable salaries (from federal as opposed to municipal governments). another factor is that participation in pmm by brazilian doctors for a minimum of one year conferred an advantage in competition to enter residency in other, "more prestigious" medical specialties. the finding that expanding supply of primary care doctors is associated with reductions in amenable mortality is concordant with evidence showing mortality reductions (including amenable [10] , cardiovascular [12] and infant mortality [35, 36] ) following esf expansion. it is also inline with broader international evidence on health benefits from expanding primary care services [37, 38] and the relationship between hrh and health outcomes [39] . the findings also align with evidence showing reductions in hospitalisations following pmm introduction [20, 21, 28, 29] and support a causal interpretation of population health improvement. mortality reductions could come from a range of mechanisms. primary care's role in prevention and resolving basic health needs is important and evidence shows pmm improved access, satisfaction, service quality, and utilisation [18, 19, 21] . specifically, reductions in respiratory mortality identified could stem from vaccination and access to antibiotics [40, 41] . mortality benefits could also accrue through increased referral to hospitals with evidence demonstrating pmm's role in increasing referrals [21] . however, reductions in mortality were small and there may be reasons why other causes of death were not significantly associated with pmm introduction. a few new doctors across a large area may not have substantially improved healthcare access or quality if there were existing health professionals (including nurses and community health workers) already providing care. some amenable conditions, such as neoplasms and maternal outcomes may be more amenable to secondary care. also, wider factors likely constrained primary care effectiveness including weak secondary care and a need to address wider social determinants of health [42] . there are limitations pertinent to this study. firstly, the analytical approach was ecological, prohibiting individual inference and limiting causal interpretation. however, the approach was robust, has been employed by similar studies [10, 11, 21, 28, 29, 43] , exploits the quasi-experimental nature of the programme, and provides stronger evidence over most other observational studies. sensitivity analyses demonstrate the robustness of the findings to alternative specifications in covariates and time trends. using municipalities as the unit of analysis may also underestimate programme effects if there is targeting to certain populations in municipalities, and smaller units of analysis such as health units could be appropriate in future studies [44] . secondly, there is potential for bias from data errors and manipulation, and modelling specifications. all data sources come from administrative sources considered of high quality, and sensitivity analyses point to the robustness of the findings. thirdly, potential bias can come from comparing pmm and non-pmm receiving municipalities given they may be different in certain respects. other studies employing the same methods point to the validity of the assumptions underpinning the analysis [21, 29] , and descriptive trends show parallel trends at baseline (see additional file 1). event study approaches further demonstrate the validity of these assumptions (see additional file 1). fourthly, the amenable mortality metric is limited as it also includes conditions sensitive to secondary care and may have limited identification of mortality effects directly related to primary care. fifthly, the pmm may have prompted better recording and doctor allocation by local health system managers, and the substitution effect could partly have come from absent doctors being removed from the system. evidence is growing that large-scale health system interventions to address hrh supply shortages can deliver health gains [1, 20] . however, this study demonstrates the importance of developing and adhering to comprehensive needs-based criteria for hrh allocation. the pmm could have delivered a near 30% increase in primary care doctors (a peak of 18,000 pmm doctors added to the 61,000 primary care doctor workforce in brazil during 2013), but the actual increase was only 12.2% as nearly two thirds of pmm doctors substituted existing primary care doctors. the programme did not deploy a formal, comprehensive needs-based approach for doctor allocation [22] and widespread allocation of pmm doctors to non-prioritised municipalities in addition to local substitution effects mean full health benefits of pmm were not realised. improved targeting and implementation of hrh interventions is needed to maximize benefits and to drive progress towards uhc and the sdgsespecially in lmics. political, administrative and financial factors likely undermined the pmm's effectiveness in brazil, but a wider question remains around the longer-term sustainability of programmes which import foreign health professionals to address domestic shortages in hrh. this was an issue for the pmm with the withdrawal of all cuban doctors by the cuban government in november 2018. the introduction of cuban doctors was an "emergency" component of the pmm, and there were efforts to primary care clinics and training positions for doctors. despite funding shortages, these longer-term sustainable solutions to appropriately train and distribute sufficient high-quality professionals domestically must remain a key priority. in december 2019, brazil introduced the "medicos pelo brasil" (doctors for brazil) programme to replace the pmm. it aims fill 18,000 positions with brazilian doctors in underserved areas incentivized with higher salaries for brazilian doctors and increased training. however, the despite the departure of the cuban doctors, many positions remain unfilled and the 2020 covid-19 pandemic in brazil has significantly disrupted plans to recruit brazilian doctors, with some cuban doctors returning to take over empty positions. great uncertaintly remains over how future policies will tackle brazil's sizeable inequalities in hrh. furthermore, the brazilian government has introduced deep austerity measures restricting public health expenditures for the next 20 years [45] . this is likely to a have major impact on financing for hrh in the future and, combined with withdrawal of cuban doctors, negative impacts on population health [46, 47] . the recent entry of over 35,000 doctors into primary care in brazil through pmm serves as an internationally important natural experiment in hrh policy. the widespread allocation of pmm doctors to non-priority areas and local substitution effects undermined programme impacts, including contributing to relatively modest reductions in amenable mortality. policymakers should recognize the importance of developing policies to expand hrh provision in improving health, but must prioritize actions to maximize the benefits and ensure policy effectiveness including developing and implementing comprehensive needs-based criteria. supplementary information accompanies this paper at https://doi.org/10. 1186/s12913-020-05716-2. abbreviations pmm: more doctors programme; sdgs : sustainable development goals; hrh : human resources for health; lmics : low-and middle-income countries; esf : estratégia saúde da família; gdp : gross domestic production; fte: full time equivalents mh, fs, cm contributed to interpretation of the findings. th wrote the initial draft of the manuscript. all authors contributed to subsequent revisions and edits, and provided intellectual inputs. all authors approved the submitted versions (and modified revisions). all authors agreed both to be personally accountable for their own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. the funders had no role in study design; data collection, analysis, and interpretation; report writing; and paper submission. all data used in this study are available from public sources (see citations in text), but data used that support the findings of this study are available from the corresponding author upon reasonable request. human resources for health and universal health coverage: fostering equity and effective coverage building economic recovery, inclusive development and social justice. geneva: switzerland international labour office (ilo) implementation research: towards universal health coverage with more doctors in brazil characteristics of the distribution of doctors in the mais médicos (more doctors) program in the states of brazil's northeast the end of brazil's more doctors programme? the mais médicos (more doctors) program: the placement of physicians in priority municipalities in brazil from human resources for health: overcoming the crisis necessidade de saúde insatisfeita no brasil: uma investigação sobre a não procura de atendimento brazil's family health strategy -delivering community-based primary care in a universal health system large reductions in amenable mortality associated with brazil's primary care expansion and strong health governance association between expansion of primary healthcare and racial inequalities in mortality amenable to primary care in brazil: a national longitudinal analysis impact of primary health care on mortality from heart and cerebrovascular diseases in brazil: a nationwide analysis of longitudinal data major expansion of primary care in brazil linked to decline in unnecessary hospitalization brazil's family health strategy: factors associated with programme uptake and coverage expansion over 15 years mais médicos program: provision of medical doctors in rural, remote and socially vulnerable areas of brazil impacto do programa mais médicos na redução da escassez de médicos em atenção primária à saúde mais medicos program: an effective action to reduce health inequities in brazil the implementation of the mais médicos (more doctors) program and comprehensiveness of care in the family health strategy evaluation of user satisfaction and service responsiveness in municipalities enrolled in the mais médicos (more doctors) program addressing inequalities in medical workforce distribution: evidence from a quasi-experimental study in brazil assessing the impact of more doctors' program on healthcare indicators in brazil resource allocation for health equity: issues and methods why do health labour market forces matter? bull world health organ mais médicos (more doctors) program a view from england cost of providing doctors in remote and vulnerable areas: programa mais médicos in brazil using natural experiments to evaluate population health interventions: new medical research council guidance measuring the health of nations: updating an earlier analysis. health aff (millwood) more doctors, better health? evidence from a physician distribution policy evaluating the impact of physicians' provision on primary healthcare: evidence from brazil's more doctors program primary care and avoidable hospitalizations: evidence from brazil the combined effects of the expansion of primary health care and conditional cash transfers on infant mortality in brazil does expanding primary healthcare improve hospital efficiency? evidence from a panel analysis of avoidable hospitalisations in 5506 municipalities in brazil how much should we trust differencesin-differences estimates? rotatividade da força de trabalho médica no brasil. saúde debate going to scale with community-based primary care: an analysis of the family health program and infant mortality in brazil the health effects of decentralizing primary care in brazil the contribution of primary care to health and health systems in low-and middle-income countries: a critical review of major primary care initiatives the impact of primary healthcare on population health in low-and middle-income countries human resources and health outcomes: crosscountry econometric study infant mortality due to acute respiratory infections: the influence of primary care processes antibiotic prescribing and outcomes of lower respiratory tract infection in uk primary care perceptions of city health managers about the provision and activity of physicians from the more doctors program. interface-comun saúde educ smoke-free legislation and neonatal and infant mortality in brazil: longitudinal quasi-experimental study more doctors recruitment program: a new approach to overcome inequalities in human resources (programa más médicos: cómo evaluar el impacto de un enfoque innovador para superar las inequidades en recursos humanos) child morbidity and mortality associated with alternative policy responses to the economic crisis in brazil: a nationwide microsimulation study mortality associated with alternative policy options for primary care and the mais médicos (more doctors) program in brazil: forecasting future scenarios mortality associated with alternative primary healthcare policies: a nationwide microsimulation modelling study in brazil springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations not applicable. 6 secretaria estadual de saude paraíba, joão pessoa, pb, brazil.received: 1 june 2020 accepted: 4 september 2020 key: cord-004345-7s2m9v2k authors: ishak, ricardo; de oliveira guimarães ishak, marluísa; vallinoto, antonio carlos r. title: the challenge of describing the epidemiology of htlv in the amazon region of brazil date: 2020-02-14 journal: retrovirology doi: 10.1186/s12977-020-0512-z sha: doc_id: 4345 cord_uid: 7s2m9v2k htlv-1 was the first described human retrovirus and was soon found to be associated with severe clinical diseases, including a devastating lymphoma/leukemia and other inflammatory diseases. although htlv-2 is not usually pathogenic, it is widely distributed among native indian populations in brazil, particularly in the amazon region of the country. presently, htlv spreads mainly by the sexual route and from mother to child, and virus persistence is an active biological factor aiding its transmission. recently, the use of illicit drugs has been shown to be an additional risk factor, showing the influence of new habits on the epidemiology of htlv in the region. despite the detection of the virus in several different populations in the amazon region of brazil for almost 30 years, the exact prevalence of htlv-1/2 is not well defined. the original biases in sampling and the selection of epidemiologically unsuitable populations were commonly repeated in most prevalence studies, generating unreliable and conflicting figures that do not represent the actual prevalence of htlv. the improvements in clinical and laboratory facilities have resulted in the description of several clinical manifestations that were previously unknown in the region. the extent of the spread of the virus must be defined in this region, which is the largest geographical area of the country. as prophylaxis advances toward the use of vaccines against htlv-1, it is important to determine who is at risk of being infected and developing a disease to successfully implement preventive measures, particularly as proposals are made to eradicate the virus among humans. human t cell lymphotropic viruses 1 and 2 (htlv-1 and htlv-2) are medium-sized virus particles (80-120 nm) belonging to the family retroviridae, genus deltaretrovirus [1] . presently, there are six molecular subtypes (namely, a, b, c, d, e and f ) of htlv-1 [2] [3] [4] and four (a, b, c and d) of htlv-2 [5] [6] [7] [8] . two other types, htlv-3 and htlv-4, have been described [9] as examples of cross-species transmission in a geographically isolated forest area in cameroon, but so far, neither have been detected elsewhere or have spread further [10, 11] . retroviruses share similar biological and replicative properties, including the evolutionary aspect of viral and cell nucleic acid integration, viral persistence, viral latency and vertical transmission to the offspring. htlv integrates the transcribed rna as a dna provirus into the cell nucleic acid [12] [13] [14] [15] [16] , and this simple evolutionary procedure leads to the persistence of the virus and its maintenance in nature and has serious implications for the different clinical and epidemiological outcomes of the infection and diseases associated with the virus. the wide array of clinical outcomes shows the target complexity within the human host (including the cns, blood, lungs, eyes, muscles, bladder and skin), and several medical specialties have to be involved in the care and treatment of infected and diseased persons [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] . htlv is an ancient infection in humans and alternates between persistence and productive cycles, which favors an effective mechanism involving vertical and horizontal transmission. according to the geographical environment and behavioral risk factors, the increased risk of transmission of the virus increases the prevalence and incidence of infection and disease [6, [28] [29] [30] [31] [32] . viral dispersion in the human body leads to the infection of several biological fluids, including the blood, semen, vaginal fluid, and milk and results in its vertical transmission from mother to child (via the placenta and perinatal breast feeding), the injection of drugs, the transfusion of blood and its components, the transplantation of organs and the engagement in sexual relations [29, [33] [34] [35] [36] [37] [38] . each of these plays an important role in viral maintenance. the risk associated with transfusion used to be major but it decreased sharply with the introduction of strict regulatory policies regarding blood screening in brazil and elsewhere [39] [40] [41] . the recommended policy of avoiding breastfeeding in mothers who carry the virus is generally followed in urban areas and is an efficient procedure whereby transmission is reduced. vertical transmission is common and is probably the most important route for the maintenance of htlv within epidemiologically closed communities, as seen with htlv-2c among indians communities in the amazon area of brazil and in urban areas [6, 33, [42] [43] [44] . among the guaymi in panama, there are relatively more infected children born from infected mothers [28, 45] , and among the kubenkokre, kayapo villagers in the amazon region of brazil, familial cluster studies have showed the transmission of the virus crossing one or more generations, and more than 20% of the children under 9 years of age are infected [6] . molecular evidence has clearly showed that the virus is transmitted from mother to child among isolated indian tribes, which illustrates the importance of the mechanism for the maintenance of the high endemicity of the virus [33, 36] . the geographical distribution of the virus is influenced by the transmission route used. in north america, htlv-2 was probably spread from american indians to injection drug users (idus), which resulted in the transmission of the virus to other idu communities in europe and was the most likely route that carried htlv to vietnam, during the war in 1960-1970 [46] [47] [48] [49] . in the amazon region of brazil, injecting drugs was not an important route for the spread and maintenance of htlv-1/2 in urban, nonurban, or isolated communities or in co-infection with hiv-1 [50, 51] in a clear contrast to what was usually seen in other areas of brazil, where the use of illicit drugs is a well-known risk factor for both virus infections [52] [53] [54] . more recently, high prevalence rates and levels of genetic diversity of both htlv-1 and htlv-2 were shown among illicit drug users in the state of para [55] , which is a change in the epidemiological pattern of the spread of the two viruses in the region. sexual transmission is certainly the most important transmission route for htlv-1 and htlv-2 and serves as an efficient mechanism for the spread of htlv-2c among native indian groups [6, 28, 56] . in urban areas, htlv infection is more common among women [42, 57, 58] . within epidemiologically closed communities such as indian populations, the distribution of antibodies against htlv shows that the prevalence increases with increasing age and is not different between males and females; this is evidence of an equal efficiency of transmission from men to women and from women to men [6, 28, 56] with the aid of vertical transmission acting by chance to infect both sexes equally. it is worth mentioning that it is not commonly observed in urban areas [42] . the description of htlv-1 and htlv-2 soon led to seroepidemiological studies based on the detection of antibodies against htlv, which is the usual approach to determine the initial prevalence rates of htlv according to geographical locations, age and sex, among other variables. few studies have been conducted strictly with controlled populations to verify the published information from the 1980s and 1990s. consequently, there have been few attempts to establish the trends in prevalence and incidence rates and the spread of htlv in brazil and, particularly in the amazon region of the country. htlv-1 was described in 1980, and htlv-2 was described in 1982 [59] [60] [61] [62] . soon, knowledge of their geographical distribution was expanded through the production of seroepidemiological data, which clearly defined the low prevalence (up to 1%) but almost universal presence of htlv-1 among specific populations (in europe, the americas, the caribbean, and sub-saharan africa), reaching more than 30% in some areas of southern japan [63] [64] [65] [66] . htlv-2, however, showed a distribution limited to intravenous drug users in the usa, europe, southeast asia and among american indians from north america to south america as well as in the pygmy tribes in central africa [6, [47] [48] [49] [66] [67] [68] [69] [70] [71] [72] . the prevalence rates were generally low (except for the hyperendemicity among some amazonian indian communities), and the association with disease was substantial with htlv-1 and not usually common with htlv-2 [73] . in brazil, associated diseases were initially described in different geographical areas and in specific groups, including blood donors and patients with hematological and neurological diseases [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] . in the amazon region of brazil, htlv-1 and htlv-2 infections were primarily described [63, [84] [85] [86] , and soon their geographical dissemination expanded [6] . in 1998, htlv-2 was detected for the first time outside native indian communities, and both viruses were found in blood donors [82] and hiv-1 carriers [50] . the first cases of diseased persons were described with htlv-1-associated myelopathy/tropical spastic paraparesis (ham/tsp) among persons residing on marajo island [83] , and the presence of both viruses on the east coast of the island was also identified on afro-descendants [87] . htlv-1 was described among sex workers, and for the first time, there was a clear geographical link when the virus was identified among japanese immigrants in the amazon originating from kyushu, a highly endemic area of htlv-1 in japan [88] . htlv human infections in the amazon region of brazil have been recorded by several studies that considered widely different populations, including blood donors, pregnant women, urban familial aggregates and native indigenous people. these investigations comprise the epidemiological picture in the north region of the country and will be presented and discussed further in the following sections. the amazon is a large geographical area involving six countries, and brazil holds the largest area in the system. the amazon region of brazil (arb) involves nine federative states and an area of 5.1 million km 2 , which represents 60% of the country but is inhabited by approximately 15% of the brazilian population. there is a large difference in demographic, social, cultural and development between the arb and the rest of the country, which is evidenced in some commonly used markers related to the health and education of the population and its level of welfare and development. historically, the arb was always left behind by policies given that the population of the region represents only 13% of the gross internal revenue of the country, has a higher rate of illiteracy (12.9% vs. 10.2%), a slightly higher infant mortality rate (18.6 vs. 15.9 per 1000) and a lower life expectancy (72 vs. 76 years) in comparison to the other areas of brazil [89] . on the other hand, the arb is a unique geographical area, considering the diversity of humans and other living species. approximately half of the so far undescribed living organisms on earth (plants, vertebrates, and microorganisms, among others) reside within the arb [90] . the history of htlv is a fascinating one regarding its possible origin in the african continent and its spread in different directions according to human migration routes [4] , and the arb is of paramount importance because of the presence of a specific strain of the virus that originated during human migration into the area and its further dissemination to other geographical areas in the country and abroad [36, 51, [91] [92] [93] [94] [95] [96] [97] . human infections by htlv in the amazon region of brazil have been recorded by several studies involving blood donors [82, [98] [99] [100] [101] [102] , pregnant women [103] [104] [105] [106] , urban familial aggregates [42] and native indians [6, 56] (fig. 1) . the isolation of htlv-1 and htlv-2 led to the manufacturing of serological assays to detect human antibodies against the viruses, and several studies were immediately performed describing prevalence rates around the world. south american countries reported quite different figures with large variations, including in argentina (0.07%), chile (0.73%), venezuela (6.8%), colombia, where the prevalence was higher in low geographical areas (4.3%) than in higher areas (0.73%) of the country, and in french guiana (6.7-13.1%) [107] [108] [109] [110] . it is important to bear in mind that these figures are rarely comparable as there are no uniformity of the different population groups investigated (age, sex, sampling, laboratory assays, among others). it is relevant to mention that the same variables are the cause to find such conflicting figures also described in brazil where the mean prevalence was initially thought to be approximately 0.41%, but there was a large range of prevalence rates from 0.08% in manaus and florianopolis to 1.35% in salvador [98] . it was common to use serological assays prepared with different strains of htlv and different targets of the reagents to detect the antibodies, and this technique is one of the possible reasons for such a variation in the figures found. in a second round of prevalence studies, a more comprehensive investigation was conducted with national public blood banks [100] , and the figures were found to be clearly different. there was a range from 0.4/1000 in the state of santa catarina (southern part of the country) to 10/1000 in the state of maranhao (in the northeast). in the amazon region of brazil, the prevalence ranged from 1/1000 in the state of rondonia to 9.1/1000 in the state of para [100] . for the purpose of the geopolitical division of the country and economic development, the so-called amazonia legal includes three other states: maranhao, tocantins and mato grosso. some of the present information and discussion will also include the state of maranhao. the main issue of concern presented is the large variation obtained by the different investigations conducted in the same geographical area. the data include the states in the north region of the country, but the results are not different from those in the rest of the country. the discrepancy is shown in table 1 , which summarizes the figures obtained in the different studies. in rio branco (acre), the investigation of htlv among blood donors showed that using two enzyme immunoassays, the results were significantly different (0.66% vs. 0.11% of 11,121 samples); the western blot results confirmed the presence of antibodies in 8 samples for htlv-1 and 2 for htlv-2. pcr results confirmed one htlv-1 and one htlv-2 reaction. the study shows the nature of conflicting results when comparing those with later results: 0.09% [99] and 0.5% [100] . mota-miranda et al. [101] investigated the molecular epidemiology of htlv-1 and described a prevalence rate of 0.46% among blood donors in 2004, although the sample was smaller than the first investigation by the local group. the state of acre is an endemic area for malaria, an additional variable that might add confusion because of the misinterpretation of results owing to cross-reactions against htlv-1 detected in patients infected with plasmodium sp. [111] . even though, a prevalence of 0.73% was detected among the general population of cruzeiro do sul, where malaria is endemic. there was a strong expectation of high prevalence rates in the state of acre considering the indians racial mixture of the general population, but so far, there is no evidence of wide distributions of the two viruses. in manaus (amazonas state), the results are also conflicting. the initial prevalence was set at 0.08% [98] and was later described as 0.53% [100] and 0.14% [112] for htlv-1/2 among blood donors in urban areas. two other relevant investigations showed that htlv infection was not present among pregnant women [105] or patients presenting with skin diseases (including dermatitis), leishmaniasis and leprosy [112] . more recently, data were published related to a retrospective prevalence of antibodies in a large group of blood donors (n = 87,402) who were initially screened from 2001 to 2003; however, only 24 persons were confirmed to be infected by htlv-1 and htlv-2, which shows the low prevalence of infection in the city of manaus [113] . the presence of the virus in different areas and populations in the state of amapa has been investigated a few times, and low prevalence rates of infection (0.71%) have been found among blood donors [100] . the viruses were not found in hiv-1 infected persons [114, 118] or in a quilombo (afro-descendants in isolated communities that were originally founded by escaped slaves); however, htlv-1 was found to be present (5/30) among individuals seeking a serological diagnosis in a public health laboratory [114] . in sao luiz, the capital city of the state of maranhao, the highest prevalence rate (1%) among blood banks in brazil was identified [100] , but the prevalence rate among pregnant women ranged from 0.34% (htlv-1, 0.19% and htlv-2, 0.15%) [104] to 0.7% (htlv-1 only) more recently described [115] . retrospective information on blood donors showed that only 0.15% among more than 365,000 persons tested in the period 2003-2009 were positive for htlv-1/2 [102] , however only 53 persons confirmed the seroreactivity. the frequencies of the identification of both viruses are not significantly different, but again the general prevalence showed figures that are somewhat lower than what was usually expected and previously described in the state of maranhao. the state of para has been the site of the majority of epidemiological studies intending to define prevalence rates of antibodies against htlv-1/2 with a variety of different populations, and several conflicting results have been obtained. the initial figures indicated that the prevalence rates measured by immunoenzymatic assays ranged from 3.6% to more than 30% for htlv-1, mostly among indians populations [84, 85] , that the rate was 0.91% among those undergoing blood donation screening [100] . a large distribution of htlv-2 was shown among indians communities not only in the state of para but also in the amazon area of brazil, reaching confirmed prevalence rates of more than 40% [6, 51, 56, 63] among some indian communities and the detection of a new molecular subtype (htlv-2c) that was soon also described in urban areas outside of the arb [6, 33, 50, 51, 116] . prevalence studies also provide interesting information, such as the description of htlv-2b among blood donors in belém, which stresses the need for ongoing molecular epidemiology investigations [116] . a comprehensive investigation detected htlv-1 among 0.3% (n = 39) of 13,382 pregnant women in belém and one person infected with htlv-2 [103] . later, another prevalence rate of 0.61% was detected in pregnant women in belém [106] . a prevalence rate (4.7%) of antibodies against htlv, detected by enzyme immune assay, was described among residents along the shores of the tucurui hydroelectric power plant [117] . this was a rather high figure for urban communities, however there was no confirmation of reactivity by other laboratory methods. the most recent investigation in belém considered the prevalence of antibodies against htlv among 1059 inhabitants and showed a 2% positivity for antibodies against both htlv-1 (n = 15) and htlv-2 (n = 5) [118] . two different studies dealt with htlv/hiv-1 coinfections. the first approach found a prevalence rate of 8% (12/149) for individuals, mostly males (n = 10), positive for htlv-1 (n = 4) and htlv-2 (n = 7) [50] . a later approach detected a prevalence rate of 5.1% (6/117) for co-infections [119] with htlv-1 (n = 02) and htlv-2 (n = 04), and those individuals were mostly female (n = 4). this clearly indicated the change in sex predominance in the hiv-1 epidemic in the city of belém. the initial approach of japanese immigrants did not result in htlv reactivity [85] , but later, the prevalence of 1.78% of htlv-1 was found in immigrants from kyushu residing in the arb [88] . the marajo archipelago also showed different figures according to the population group investigated. it was higher in an epidemiologically semi-closed quilombo than the average of four municipalities (1.5% vs. 0.1%, respectively) investigated [87, 94] . since the initial detection of ham/tsp in patients from the marajo archipelago, in the north region of brazil [83] , htlv-1-infected male and female patients with different signs of clinical severity of neurological disease have been described [20] . although there have been continuous descriptions of persons with other diseases, including dermatological symptoms [120] , no hematological disorders, so far, have been associated with htlv-1 infection in the arb. fairly rapid changes in the epidemiology of htlv-1/2 are occurring in the arb. a recent and extensive study was performed in the state of para, which detected an intermediate prevalence of 4.3% with almost the same frequencies of htlv-1 (n = 25) and htlv-2 (n = 19) among drug users [55] . both viruses are widely distributed in the amazon region of brazil and particularly among this population, who especially need close attention in terms of the control and prevention of infection as they are key participants in the spread of the virus. epidemiological studies in the arb, as in other areas of the country and abroad, have been plagued by imprecise sampling ("grab samples" was common), which generated inadequate and conflicting results among several studies. groups of sub-populations were consistently chosen, with the equivocal assumption of a general figure for most of the region, leading to a selection bias that rendered untrustworthy results. the selection of blood donors, the selection of diseased population subgroups, and the retrospective collection of data are some of the examples that should be avoided in future prevalence studies. relevant population groups should be selected and preferably using multiple centers of study working together to increase sample size. it is relevant to stress that confirmatory tests should be always used to make sure the information is not equivocal and the absence of correct information should be put ahead to avoid misinterpretations. urban populations should be the optimal target to answer important questions such as the following: who is mostly affected by this neglected infection? who should receive future preventive measures such as vaccines? which risk factors are relevant for the transmission of the virus? htlv-1 is an important human pathogen and the only human retrovirus associated with a large array of diseases, including lymphoma/leukemia. however, in the possible event of the development of a vaccine in the near future, health authorities will not be able to immediately define the population at risk who should receive it, either in the arb or in other areas of the country. new and authoritative epidemiological information should be gathered to gauge the actual need for such a product. australian aboriginal people are examples of persons at high risk for morbidity and mortality associated with the wide dissemination and high prevalence of htlv-1. respiratory diseases recently also described in the arb [121] are new and dangerous facets of the infection that can truncate productive lives, which is a compelling reason to revitalize htlv-1 epidemiological studies in the arb, elsewhere in the country and worldwide. small epidemiologically closed or semi-closed human aggregates are easier with regard to the implementation of preventive measures, although transmission in such communities is further enhanced by the mother to child transmission route in utero, during birth and during breast feeding both perinatal and after birth, which corroborates the formation of familial aggregates. the most recent report from our laboratory has shown that asurini and arawete indian tribes have remained free from htlv-1/2 infections due to cultural and social isolation from the infected neighboring tribes and villages [122] . indian communities from the north region of brazil usually experience hyperendemic infections with htlv-2, which is less pathogenic than htlv-1; this is a more favorable situation compared to what is found among native aboriginal people in australia, where hyperendemicity exists with the more pathogenic htlv-1 [30, 123] . it is reasonable to infer that the general prevalence of the virus should be decreasing because of the general policies regarding testing blood donations and some efforts to disseminate general knowledge of the virus, but so far this has not been substantiated, as conflicting prevalence results generate confusion regarding the adequate delivery of information. national associations of htlv-infected persons are active and give full support to the elimination of the virus, but their messages are not always disseminated through the appropriate channels. although the existing preventive campaigns are not aggressive, they should receive full official support to attain success in the future, particularly as proposals are being made with regard to virus eradication [124] . taxonomy history: primate t-lymphotropic virus 1 phylogenetic subtypes of human t-lymphotropic virus type i and their relations to the anthropological background molecular epidemiology of htlv type i in japan: evidence for two distinct ancestral lineages with a particular geographical distribution dating the origin of the african human t-cell lymphotropic virus type-i (htlv-i) subtypes multiple isolates and characteristics of human t-cell leukemia virus type ii identification of human t cell lymphotropic virus type iia infection in the kayapo, an indigenous population of brazil identification and characterization of a new and distinct molecular subtype of human t-cell lymphotropic virus type 2 african origin of human t-lymphotropic virus type 2 (htlv-2) supported by a potential new htlv-2d subtype in congolese bambuti efe pygmies emergence of unique primate t-lymphotropic viruses among central african bushmeat hunters short communication: no evidence of htlv-3 and htlv-4 infection in new york state subjects at risk for retroviral infection short communication: absence of evidence of htlv-3 and htlv-4 in patients with large granular lymphocyte (lgl) leukemia viral rna-dependent dna polymerase: rna-dependent dna polymerase in virions of rna tumour viruses viral rna-dependent dna polymerase: rnadependent dna polymerase in virions of rous sarcoma virus htlv-1-infected t cells contain a single integrated provirus in natural infection morphology and ultrastructure of retrovirus particles retroviruses integrate into a shared, non-palindromic dna motif isolated bladder dysfunction in human t lymphotropic virus type 1 infection inflammatory manifestations of htlv-1 and their therapeutic options update on neurological manifestations of htlv-1 infection neurological manifestations in individuals with htlv-1-associated myelopathy/tropical spastic paraparesis in the amazon human t lymphotropic virus and pulmonary diseases turning a blind eye: htlv-1-associated uveitis in indigenous adults from central australia systemic diseases in patients with htlv-1-associated uveitis adult t-cell leukemia/lymphoma-related ocular manifestations: analysis of the first large-scale nationwide survey a case of adult t-cell leukemia/lymphoma complicated with bilateral chylothorax crusted (norwegian) scabies as a strong marker of adult t-cell leukemia/lymphoma in htlv-1 infection htlv-1-host interactions facilitate the manifestations of cardiovascular disease isolation of human t-cell lymphotropic virus type 2 from guaymi indians in panama epidemiological aspects and world distribution of htlv-1 infection human t-lymphotropic virus type 1 infection in an indigenous australian population: epidemiological insights from a hospital-based cohort study revisiting human t-cell lymphotropic virus types 1 and 2 infections among rural population in gabon, central africa thirty years after the first analysis risk factors associated with htlv-1 vertical transmission in brazil: longer breastfeeding, higher maternal proviral load and previous htlv-1-infected offspring molecular evidence of mother-to-child transmission of htlv-iic in the kararao village (kayapo) in the amazon region of brazil seminal fluid enhances replication of human t-cell leukemia virus type 1: implications for sexual transmission molecular determinants of human t-lymphotropic virus type 1 transmission and spread htlv-2: uma infecção antiga entre os povos indígenas da amazônia brasileira. rev pan-amazônica de saúde htlv-1 infection in solid organ transplant donors and recipients in spain mother-to-child htlv-1 transmission: unmet research needs decline in prevalence and asymmetric distribution of human t cell lymphotropic virus 1 and 2 in blood donors, state of minas gerais human t-lymphotropic virus type 1 and type 2 seroprevalence, incidence, and residual transfusion risk among blood donors in brazil during infection with human t-lymphotropic virus types-1 and -2 (htlv-1 and -2): implications for blood transfusion safety familial transmission of human t-cell lymphotrophic virus: silent dissemination of an emerging but neglected infection mother-to-child transmission of htlv-1 epidemiological aspects, mechanisms and determinants of mother-to-child transmission silent dissemination of htlv-1 in an endemic area of argentina. epidemiological and molecular evidence of intrafamilial transmission evidence for sexual and mother-to-child transmission of human t lymphotropic virus type ii among guaymi indians nucleotide sequence and restriction fragment-length polymorphism analysis of human t-cell lymphotropic virus type ii (htlv-ii) in southern europe: evidence for the htlv-iia and htlv-iib subtypes short communication: identification and molecular characterization of human t lymphotropic virus type ii infections in intravenous drug abusers in the former south vietnam evolutionary rate and genetic heterogeneity of human t-cell lymphotropic virus type ii (htlv-ii) using isolates from european injecting drug users high rate of human t lymphotropic virus type iia infection in hiv type 1-infected intravenous drug abusers in ireland serological evidence of htlv-i and htlv-ii coinfections in hiv-1 positive patients in belém, state of pará. brazil molecular epidemiology of human t-lymphotropic virus type ii infection in amerindian and urban populations of the amazon region of brazil epidemiological characteristics of htlv-i and ii co-infection in brazilian subjects infected by hiv-1 risk factors for human t cell lymphotropic virus type i among injecting drug users in northeast brazil: possibly greater efficiency of male to female transmission assessing risk behaviors and prevalence of sexually transmitted and blood-borne infections among female crack cocaine users in salvador-bahia, brazil human t-lymphotropic virus 1 and 2 among people who used illicit drugs in the state of pará high prevalence of human t-lymphotropic virus 2 (htlv-2) infection in villages of the xikrin tribe (kayapo), brazilian amazon region current prevalence of htlv-1 in japan as determined by screening of blood donors prevalence of human t-cell lymphotropic virus and the socio-demographic and risk factors associated with the infection among post-natal clinics women in zaria detection and isolation of type c retrovirus particles from fresh and cultured lymphocytes of a patient with cutaneous t-cell lymphoma isolation of a new type c retrovirus (htlv) in primary uncultured cells of a patient with sézary t-cell leukaemia a new subtype of human t-cell leukemia virus (htlv-ii) associated with a t-cell variant of hairy cell leukemia history of the discoveries of the first human retroviruses: htlv-1 and htlv-2 endemic human t cell lymphotropic virus type ii infection among isolated brazilian amerindians first description of endemic htlv-ii infection among venezuelan amerindians findings from the miyazaki cohort study the epidemiology of htlv-i in europe human t cell lymphotropic virus types i and ii in intravenous drug users in san francisco: risk factors associated with seropositivity htlv-ii endemicity among guaymi indians in panama htlv-ii seroprevalence in pygmies across africa since 1970 what is the situation of human t cell lymphotropic virus type ii (htlv-ii) in africa? origin and dissemination of genomic subtypes low prevalence of htlv-ii in mayan indians in the yucatan peninsula characteristic distribution of htlv type i and htlv type ii carriers among native ethnic groups in south america human t lymphotropic virus type ii (htlv-ii): epidemiology, molecular properties, and clinical features of infection seroepidemiologic survey for antibodies to human retroviruses in human and non-human primates in brazil tropical spastic paraparesis in northeastern brazil adult t-cell leukaemia/lymphoma in brazil and its relation to htlv-1 clinical and demographic features of htlv-1 associated myelopathy/tropical spastic paraparesis (ham/tsp) in rio de janeiro, brazil htlv-1 and myelopathy in salvador (northeastern brazil): a case control study seroepidemiology of human t-cell lymphotropic virus type i/ii in northeastern brazil human t-cell leukemia viruses: epidemiology, biology, and pathogenesis htlv-i and htlv-ii infections in hematologic disorder patients, cancer patients, and healthy individuals from rio de janeiro, brazil detection of htlv-iia in blood donors in an urban area of the amazon region of brazil htlv-i associated myelopathy in the northern region of brazil prevalence of human t cell leukemia virus-i (htlv-i) antibody among populations living in the amazon region of brazil (preliminary report) prevalence of htlv-i antibody among two distinct ethnic groups inhabiting the amazon region of brazil endemic transmission of htlv type ii among kayapo indians of brazil identification of human t-cell lymphotropic virus infection in a semi-isolated afro-brazilian quilombo located in the marajó island serological and molecular evidence of htlv-i infection among japanese immigrants living in the amazon region of brazil half-earth: our planet's fight for life human t-cell lymphotropic virus type ii in guaraní indians, southern brazil molecular evidence of htlv-ii subtype b among an urban population living in south brazil infectious agents as markers of human migration toward the amazon region of brazil human t-lymphotropic virus 1aa circulation and risk factors for sexually transmitted infections in an amazon geographic area with lowest human development index the first survey of human t-cell lymphotropic viruses (htlv) in hiv/aids patients in santa catarina state evidence of new endemic clusters of human t-cell leukemia virus (htlv) infection in bahia :e20180244. research data, including large and complex data types • gold open access which fosters wider collaboration and increased citations maximum visibility for your research: over ready to submit your research ? choose bmc and benefit from distribution of human t-lymphotropic virus type i among blood donors: a nationwide brazilian study prevalência da infecção pelo vírus linfotrópico humano de células t e fatores de risco associados à soropositividade em doadores de sangue da cidade de rio branco heterogeneous geographic distribution of human t-cell lymphotropic viruses i and ii (htlv-i/ii): serological screening prevalence rates in blood donors from large urban areas in brazil htlv-1 infection in blood donors from the western brazilian amazon region: seroprevalence and molecular study of viral isolates seroprevalence of htlv-1/2 among blood donors in the state of maranhão descriptive study of htlv infection in a population of pregnant women from the state of pará, northern brazil high prevalence of htlv-1 and 2 viruses in pregnant women in são luis, state of maranhão prevalência de infecção por hiv, htlv, vhb e de sífilis e clamídia em gestantes numa unidade de saúde terciária na amazônia ocidental brasileira seroprevalence of hiv, htlv, cmv, hbv and rubella virus infections in pregnant adolescents who received care in the city of belém a survey of the human t-cell lymphotropic virus type i (htlv-i) in south-western colombia human t-lymphotropic virus type i: new risk for chilean population demographic and familial characteristics of htlv-i infection among an isolated, highly endemic population of african origin in french guiana first seroepidemiological study and phylogenetic characterization of human t-cell lymphotropic virus type i and ii infection among amerindians in french guiana occurrence of cross-reactivity to htlv-1/2 antigens in patients with malaria from an endemic area of the brazilian amazon region absence of htlv-1/2 infection and dermatological diseases in manaus, state of amazonas prevalence of human t-lymphotropic virus type 1 and 2 among blood donors in manaus, amazonas state epidemiologia molecular do vírus linfotrópico de de células t humanas, htlv-1/2 no estado do amapá-brasil (molecular epidemiology of htlv-1/2 in the state of amapa-brazil) molecular detection of human t cell lymphotropic virus type 1 in pregnant women from maranhão state, brazil caracterização molecular do htlv-1/2 em doadores de sangue em belém, estado do pará: primeira descrição do subtipo htlv-2b na região amazônica environmental impact and seroepidemiology of htlv in two communities in the eastern brazilian amazon moderada endemicidade da infecção pelo vírus linfotrópico-t humano na região metropolitana de belém molecular characterization of human t-cell lymphotropic virus coinfecting human immunodeficiency virus 1 infected patients in the amazon region of brazil dermatological manifestations in patients with human t-cell lymphotropic virus at a reference service in amazon ct chest and pulmonary functional changes in patients with htlv-associated myelopathy in the eastern brazilian amazon isolation of the arawete and asurini indians keeps the tribes free from htlv infection during 36 years of follow-up htlv-i among northern territory aborigines time to eradicate htlv-1: an open letter to who publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations we thank conselho nacional de desenvolvimento científico e tecnológico-cnpq and universidade federal do para. the authors declare that they have no competing interests.received: 21 november 2019 accepted: 9 february 2020 key: cord-273065-peqz7okh authors: girard, marc; nelson, christopher b.; picot, valentina; gubler, duane j. title: arboviruses: a global public health threat date: 2020-04-24 journal: vaccine doi: 10.1016/j.vaccine.2020.04.011 sha: doc_id: 273065 cord_uid: peqz7okh a conference on «arboviruses, a global public health threat» was organized on june 20–22, 2018 at the merieux foundation conference center in veyrier du lac, france, to review and raise awareness to the global public health threat of epidemic arboviruses, and to advance the discussion on the control and prevention of arboviral diseases. the presentations by scientists and public health officials from asia, the americas, europe and africa strengthened the notion that arboviral diseases of both humans and domestic animals are progressively becoming dominant public health problems in the world. the repeated occurrence of recent deadly epidemics strongly reinforces the call for action against these viral diseases, and the need for developing effective vaccines, drugs, vector control tools and strong prevention programs. declaring a dengue pandemic in the 1990 0 s was a sentinel call to action in the fight against a range of emerging arboviral diseases of humans [1, 2] . the past 50 years have seen a dramatic émergence/re-emergence of epidemic arboviral diseases [3, 4] . the recent outbreak of neurological disorders and neonatal malformations associated with zika virus (zikv) infection in latin america {5}, the yellow fever (yfv) epidemics in angola and brazil with importation to china [6] , the ever-expanding west nile virus (wnv) epidemic in the americas [7] , the recent emergence in east africa and global spread of chikungunya virus (chikv) [8] , as well as the ongoing and expanding dengue virus (denv) pandemic in the tropics and subtropics [9] have reinforced the call for action in the fight against emerging and re-emerging arboviral diseases. these epidemics underscore the urgency and need for integrated control and prevention of arboviral diseases, especially those transmitted by aedes mosquitoes in urban areas [10, 11] . prevention and control strategies currently focused on vector control, including insecticide treatment, environmental management and social mobilization have not been effective in practice. it is widely recognized that no strategy alone can fully address the problem. however, some intervention tools have helped reduce the disease burden. for example, timely access to clinical services and appropriate care can reduce mortality dramatically [12] , indoor residual spraying (irs) and indoor space spraying (iss) may be effective in reducing mosquito populations and exposure to arboviruses [11] . in addition, personal protection, clinical diagnosis and management, laboratory-based surveillance and vaccination, can be effective [12] . vaccines are available to protect against japanese encephalitis and yellow fever [13] , and the first dengue vaccine, even though limited in its applications, was licensed in 2015 [14] . dr duane gubler (duke-nus medical school, singapore) reminded the audience that the frequency and magnitude of the arboviral epidemics and the extent of their geographic spread have progressively increased over time, accelerating in the past 30 years and now occurring globally in the tropics [3, 4] . https://doi.org/10.1016/j.vaccine.2020.04.011 0264-410x/ as an illustration, denvs were found in the 1960 0 s in less than 10 endemic countries and only a few thousand cases were reported each year. in contrast, in 2017 the virus had become endemic in 124 countries, causing an estimated 400 million yearly infections and 100 million symptomatic cases [9] . in the 1970 0 s, denv serotypes 3 and 4 could be found only in south-east asia. but in the early 1980 0 s, all four serotypes of denv had dramatically spread to to all regions of the tropics [9] . similarly, a new strain of chikv emerged in east africa in 2004, spreading to asia and then to the rest of the tropical world in 10 years [8] . and epidemic zikv emerged in the pacific and spread around the world in only 7 years [5] . all of these viruses are transmitted by the urban mosquito, aedes aegypti. west nile virus (wnv), transmitted primarily by bird feeding culex mosquitoes, was introduced to the western hemisphere for the first time in 1999, rapidly spreading from the east coast of the usa to the rest of the country and to canada before invading the caribbean, central and south america [7] . in 2002, 14,000 cases of wnv encephalitis in horses and 4,000 cases in humans were reported in the usa. wnv is now enzootic in the region. dr joao bosco siqueiras (institute of tropical pathology and public health, goias, brazil) described another dramatic example, that of yellow fever, which is also transmitted by aedes aegypti. the mosquito is widely prevalent in the tropics including tropical america and most countries in subsaharan africa. in 2007-2010 yellow fever emerged and expanded into the south and southeastern parts of brazil, where yellow fever vaccination was not common. then, in 2014-15, it emerged in central brazil, infecting many travelers. cases of yellow fever were exported from brazil to europe, peru and the usa. the virus continued to spread in 2017-18 into the areas of bahia, rio and sao paolo and was detected in 4266 municipalities, causing small urban epidemics [15] . the death toll increased to 235 persons in 2017 and 409 in the first half of 2018. in africa, yellow fever spread from angola to the democratic republic of congo in 2016-17, and emerged in nigeria and uganda in 2018 [16] . more dramatically, 11 cases were imported from angola to china, which is the first time in history that confirmed yellow fever was introduced to asia [6]! as outlined by dr duane gubler, the new and worrisome aspect of emerging arbovirus epidemics is that they can occur in urban centers, as was observed with dengue fever, zika, chikungunya and yellow fever. the urban vectors are aedes mosquitoes, primarily aedes aegypti, which has spread around the world in past centuries, and secondarily aedes albopictus, whose spread began in the 1980s [17] . the emergence and spread of dengue, chikungunya and zika infections actually reflect the growing geographical spread of aedes spp across all continents. the fact that arboviral diseases have become a major threat to urban populations is the result of: 1) population growth and urbanization, which results in crowding of humans, inadequate housing, waste management and accumulation of trash, including used automobile tires, plastics, tins, etc, creating ideal ecological conditions for urban aedes populations to thrive; 2) the spread of aedes spp mosquitoes around the world and throughout the tropics and subtropics; 3) the lack of effective vector control and infectious disease prevention; and 4) the globalization of air transport, which facilitates the rapid spread of pathogens and the diseases they cause (more than 3 billion passengers have travelled on air lines in the year 2018) [2, 3, 18, 19] . as these trends will continue, epidemic arboviral diseases will increasingly threaten global, national and local political and economic security and could create a global public health emergency, similar to or even greater than the current sar-cov-2 pandemic. one should not forget that over 3.6 billion people live in areas exposed to urban aedes mosquitoes. dr duane gubler also noted that since arboviral diseases represent a major threat to urban populations, it is necessary to reassess surveillance strategies. currently, surveillance systems are based on passive reporting of loosely defined clinical syndromes with infrequent laboratory confirmation. he suggested that all at-risk countries should have an enhanced passive disease surveillance system based on well-defined case definitions supported by serological and virological laboratory testing. three major arbovirus pathologies should be monitored: systemic febrile syndrome, haemorrhagic disease syndrome, and meningo-encephalitis syndrome. an active laboratory-based syndromic surveillance network is also badly needed. weekly reports by local physicians, as done in brazil, where they have turned out to be most useful, should also be encouraged. however, as discussed by dr elizabeth hunsperger (cdc, atlanta, usa), differential diagnosis in the clinical setting may be difficult, especially outside of seasonal disease, as mild and asymptomatic infections are common. as an example, laboratory testing for dengue is important in order to distinguish the disease from other febrile illnesses such as malaria, leptospirosis or influenza, other arbovirus diseases such as chikungunya, zika, west nile, japanese encephalitis or yellow fever, and even from typhoid/paratyphoid (salmonella typhi or salmonella paratyphi spp bacteria). recently, who has recommended the serotesting of individuals in dengue vaccination settings to screen out those with no evidence of past infection. each of theses objectives requires different test characteristics. standard dengue diagnostics assays include rt-pcr, virus neutralization assays, immunoassays to detect denv ns1 antigen, and assays to detect anti-denv igms [ref] . the most sensitive and specific assays are rt-pcr and the ns1 elisa assay. low-cost point-ofcare (poc) rapid diagnostic tests (rdts) are currently not adequate for the clinical and vaccination settings, while elisa, rt-pcr and other strategies with much higher levels of performance are are too slow and costly. the latter tests are needed in public health surveillance and research settings. these diagnostic approaches are instrument-dependent and require appropriate facilities and highly trained technical staff to perform complex diagnostic tests, unfortunately none of which are available in resource-limited areas. dengue diagnostics will greatly benefit from a dengue poc test that meets the who assured criteria (affordable, sensitive, specific, rapid, user-friendly and delivered to those in need) [20] . note that laboratory diagnosis of dengue can be achieved with a single serum specimen obtained during the febrile phase of the illness by testing for denv nucleic acid, non-structural protein 1 (ns1) and anti-denv igms. the current poc rdts detect both anti-denv igms and iggs as well as the ns1 antigen. this has the potential to change the current situation in resource-limited areas and improve dengue clinical management. denv viremia occurs for up to 12 days following the onset of fever, and anti-denv igms begin to appear around 3 days after fever onset. detection of denv nucleic acid by rt-pcr is the most sensitive and specific means to confirm acute infection, but it may not necessarily reflect infectious virus as it only detects viral rna, which may persist in biologic fluids after infectious virus is cleared. immunoassays to detect denv ns1 antigen also provide acceptable levels of sensitivity and specificity. both these diagnostic approaches are instrument-dependent and require appropriate facilities to perform complex diagnostic tests. recently, it was found that apoprotein h (apo h) can be efficiently used to detect bacteria and viruses in blood samples. as described by dr francisco veas (french institute for dvelopment (ird), montpellier, france), beads coated with apo h can readily capture viruses with a glycoprotein-rich envelope such as influenza virus, ebola virus, denv and other arboviruses, or even hcv. the beads are easy to use, the process is very fast and shows high sensitivity: one can readily detect 1 pfu of virus in 5 ml of whole blood. dr rome buathong (bureau of epidemiology, dept of disease contrtol, thailand ministry of public health) reminded the audience that until the brazilian outbreak in 2015-16, zikv was a little known arbovirus presenting with a mild dengue-like illness without any major complications [21] . it initially spread from sub-saharan africa to asia without detection. thus, although the virus was present in thailand, it was not detected until may 2013, when a canadian traveler returning from thailand was diagnosed with the disease. a zikv surveillance program was launched in the country (from january 2016 to december 2018) revealing a yearly peak of zikv infection during the rainy season, occurring 6-8 weeks after the peak of dengue disease. a total of 1698 confirmed cases of zikv infection was recorded in thailand during this two year period. the age groups most affected were the 11-20 followed by the 21-30 year groups. a total of 121 cases of zikv infection was recorded in pregnant women, leading to 4 miscarriages and 4 birth abnormalities, including 3 cases of microcephaly. aedes mosquitoes in the country were found to be zikv positive, but other routes of transmission included blood transfusion and sexual intercourse. zikv rna could readily be detected from plasma, saliva and urine of infected patients. sexual transmission of zikv has been documented to occur up to three weeks after onset of illness in the male partner. shedding of the viral rna in semen has been well documented, but only 4% of semen samples that were pcr positive could be shown to contain infectious virus by cell culture. dr nikos vasilakis (university of texas medical branch) reviewed the explosive emergence of zikv in 2015-16 in the south pacific and south america, with a focus on brazil where major clinical outcomes in pregnant women were common. the alarming numbers of zikv associated microcephaly and other gestational and neonatal complications brought the virus into the spotlight. increased reporting of guillain-barré syndrome (gbs) and other neurological manifestations was also associated with zikv infections. the first association between zikv infection and microcephaly was reported in 2015 in recife, brazil where three women infected with zikv during their pregnancy delivered babies with microcephaly. it was retrospectively discovered that neurological diseases, including microcephaly, in babies born to zikv-infected mothers, had been observed in french polynesia as early as 2014. as reported by dr patricia brasil (oswaldo cruz foundation, rio do janeiro), a prospective cohort study for zikv infection in pregnant women and infants was initiated in rio de janeiro in early 2016. zikv was recovered from the amniotic fluid and placenta of the pregnant women, and also from the cerebral spinal fluid of their babies. microcephaly was observed in 4%-6% of the newborns, while structural birth defects such as hypertonicity, cardiac defects, ophtalmic abnormalities, elbow abnormality, and seizures were observed in up to 11.9% of the newborns. a follow-up of brazilian babies born to mothers infected by zikv during pregnancy showed that up to 25% had abnormal hearing or other manifestations, and 47% showed signs of abnormal behavior. at 18 months of age, only 21% of the babies displayed normal neurodevelopment. dr mauricio lacerda nogueira (faculty of medicine, sao jose do rio preto brazil) talked of the interplay between various flaviviruses. given that brazil is hyperendemic for arboviruses, there was concern that previous heterotypic flavivirus (e.g. dengue) exposure could exacerbate zika disease pathogenicity. denv antibodies (ab) bind to zikv. could they drive greater zikv replication through antibody-dependent enhancement (ade)? the phe-nomenom was initially described for denv, but it has also been found to exist for rabies virus, coxsackievirus b3, coronaviruses, and even hiv. to answer the question, a cohort of healthy volunteers in vila toninho, brazil, was followed up from 2015 to 2018, looking for evidence for a possible ade phenomenom. in spite of the fact that 74% of the cohort had denv ab at the start of the study, no significant clinical difference could be observed in zikv infections between denv ab positive and denv ab negative persons. thus, the epidemiological evidence in brazil did not support the hypothesis that previous exposure to denv infection could enhance zikv pathogenicity. by contrast, it has been reported that denv-1 and denv-2 ab might be protective against zikv infection. similarly, the presence of yfv ab has recently been associated with a better prognosis of zikv infection in pregnant women. other hypotheses, such as enhanced infectivity of zikv for aedes mosquitoes, have not been confirmed. interestingly, a a226v mutation in the e1 gene of chikv has recently been described which is associated with enhanced infectivity of the virus for aedes albopictus mosquitoes. as discussed by dr nikos vasilakis, the most convincing explanation for the sudden aggressivity of zikv lies in the discovery by yuan et al [22] in 2017 of a mutation in the prm gene of the brazilian strain of zikv, which could strongly contribute to the generation of fetal microcephaly. the mutation was also found in zikv strains from french polynesia, where numerous cases of microcephaly have been recorded, but not in virus strains from africa, where microcephaly has never been observed. dr marc lecuit (pasteur institute, paris), addressing the question of the cellular and molecular mechanisms of microcephaly, reminded the audience that, in contrast with chikv, which does not cross the placental barrier, zikv can readily penetrate and infect placental cells. inoculation of zikv in the brain of mouse embryos triggers an endoplasmic reticulum stress which perturbs the physiological unfolded protein response (upr) within apical cortical progenitor cells that control neurogenesis. sustained endoplasmic reticulum stress leads to apoptosis. thus, it is likely that, in pregnant women, zikv crosses the placental barrier, gets to the brain of the foetus and crosses the blood-brain barrier, then targets apical cortical progenitor cells, which leads to the blockade of upr and the arrest of neurogenesis, and, as an obvious consequence, to microcephaly. microcephaly has not been observed in africa; it appears to be a specific property of the brasilian zikv strain, and is most likely related to the prm mutation identified by yuan et al [22] . dr michael gaunt (london school of hygiene and tropical medicine) reported a series of experiments done on zikv and denv to identify potential genetic determinants of ade. a 10 amino acid long motif in the denv glycoprotein was identified which might be associated with ade. dr annelies wilder-smith (london school of hygiene and tropical medicine) reviewed the eu research program on zikv (the 'zikaplan'), which oversees 25 institutional global partners with plans to set up a sustainable latin american research preparedness network for emerging diseases. a longitudinal cohort study of 17,000 subjects aged 2-59 is being followed for three years in 14 different locations in brazil, to further refine the full spectrum and risk factors of congenital zika syndrome, including neurodevelopment milestones, mental retardation, etc, during the first 4 years of life. also to be addressed is whether neurological problems associated with zikv infection, such as meningoencephalitis or acute zika myelitis, are the direct consequence of zikv infection, or are mediated by immune responses. novel zikv diagnostic tests will also be developed. dr louis lambrechts (pasteur institute, paris) reminded the audience that aedes aegypti, which is distributed throughout the tropical and sub-tropical world on all continents, serves as the major vector to transmit urban arboviruses, including the 4 denvs, zikv, yfv, chikv, etc. whereas most female mosquitoes take only one blood meal a day, aedes aegypti females need multiple blood feedings every day, which makes them more efficient at transmitting epidemic disease. the comparison between aedes aegypti and ae albopictus also shows that, although ae albopictus is often more susceptible to infection by denv than ae aegypti, it appears to be significantly less efficient at transmitting the virus. in addition, factors such as the mosquito genotype, its geographical location, and the strain of arbovirus, influence the transmission dynamics of the disease. for example, zikv infection of ae aegypti mosquitoes seems to be influenced by the sequence of the ns1 protein of the virus. as reported by dr scott ritchie (james cook university, cairns, australia), the use of wolbachia infection of aedes mosquitoes has great potential to control the spread of the arboviruses they transmit. wolbachia-infected male aedes mosquitoes become sterile and, if sterile males are repeatedly introduced in a given area, the resident aedes populations can be suppressed. alternatively, wolbachia-infected male and female mosquitoes can be introduced together, which leads to a progressive replacement of the resident aedes population, which could then show a much reduced capacity at transmitting denv, zikv, chikv, yfv and possibly other viruses [23, 24] . the use of wolbachia is recommended by the world mosquito program to eliminate dengue. a trial in australia has demonstrated that, shortly after release of wolbachia-infected aedes mosquitoes, over 90% of the mosquitoes population at the site became wolbachia-infected, and the transmission of denv was stopped [25] . similar trials are being conducted in viet nam, indonesia and brazil. the fear that wolbachia infection of ae aegypti would lead to its replacement by ae albopictus seems unwarranted so far, but it requires further studies. dr joao bosco siqueira reported that brazil had suffered from a shortage of yellow fever vaccine. fortunately, the usual dose of the brazilian vaccine contains 40,000 pfu of attenuated yfv (strain 17d), when only 5,000 pfu is a sufficient protective dose [26] . it has therefore, been possible to use fractional doses of vaccine with evidence of protection and relatively no difference in reported adverse events. faced with the spread of yellow fever throughout the country, the brazilian government has updated its vaccination policy and now recommends that the entire population should be vaccinated. as part of this effort, a change in schedule for children was implemented from a single dose at 5 years of age to a 2 dose schedule with the first dose administered at 9 months and a second dose at 4 years. this effort is complicated by inadequate vaccine supply and also false rumors that the vaccine would not be protective. fake news is unfortunately powerful and, as a result, vaccine refusal has been rising in the population! as reviewed by dr in-kyu yoon (international vaccine institute, south korea), dr christopher nelson (sanofipasteur, lyon, france) and dr annelies wilder-smith, major advances in dengue research have resulted in development of new vaccines that show promise for use in dengue prevention, such as sanofi pasteur's recently licensed cyd-tdv (dengvaxia ò , sanofi pasteur, lyon, france) and six other dengue vaccine candidates in various phases of clinical trials. cyd-tdv is a tetravalent live attenuated chimeric vaccine consisting of a 17d yfv genome with the pre-membrane (pre-m) and envelope (e) genes from each of the four antigenically distinct denv serotypes. the vaccine has undergone large-scale phase 3 clinical trials in asia and latin america [13, 14] , demonstrating increasing efficacy with age and higher efficacy in baseline seropositives. efficacy was highest at preventing severe dengue and hospitalization, and moderate for overall dengue. it also varied with serotype, being higher (75-84%) for denv-3 and -4 infection, and lower for denv-1 and -2. notably, during the third year of the asian phase 3 trial, an increased risk of dengue hospitalization was seen in children aged 2-5 years. efficacy of the vaccine was only 5% or less in 2-6 years old and 65% in 6-8 years old. the vaccine was licensed in 2015 with an age indication of 9-45 years (up to 60 years of age in some countries). the cyd-tdv vaccine is now licensed in 20 countries, and has been introduced into public immunization programs in endemic areas of the philippines and brazil. the vaccine showed high efficacy and good safety in seropositive persons in the 9-45 years age group, but a risk of severe dengue was observed in individuals who were naive for denv infection at the time they were vaccinated. it was hypothesized that cyd-tdv mimics primary infection among individuals with no prior dengue infection (previously dengue-unexposed, seronegatives) and a secondary-like infection among those with prior dengue infection (previously dengue-exposed, seropositives) [14, [27] [28] [29] [30] . a retrospective case-cohort study was undertakern to analyze vaccine safety among dengue seropositive and seronegative trial participants. this work used anti-ns1 results from month 13 of follow-up that were obtained using an anti-ns1 igg elisa developed for this purpose. the data confirmed the substantial benefit of cyd-tdv vaccination in those who are dengue seropositive and aged 9 years or older, reducing symptomatic dengue, hospitalized dengue and severe dengue by~80%. however, in individuals of any age without evidence of prior dengue infection, the vaccine elicited an increased risk of severe dengue, as announced by sanofi pasteur in november 2017. the vaccine should therefore be administered only to dengue seropositive persons, which obviously implies the need for a pre-vaccination screening strategy [30] . the who sage dengue working group reviewed these data and, in april 2018, the sage committee recommended to vaccinate only those with evidence of past dengue infection (seropositives) or with medical documentation of past dengue infection. these results have implications for other dengue vaccine candidates in clinical development, and for immunization program policy and program implementation. two other dengue vaccine candidates are currently in phase 3 clinical trials: tdv, developed by the us cdc and manufactured by takeda, and tv003/005, developed by the us nih. tdv is a tetravalent live attenuated chimeric vaccine that uses an attenuated denv-2 backbone with the pre-m and e genes from each of the other three denv serotypes. the tdv vaccine is undergoing phase 3 trials in brazil, columbia, nicaragua, panama, sri lanka and thailand. preliminary phase 3 data show the vaccine is safe and has good efficacy against denv-1 and-2, but the results for denv-3 and -4 are uncertain because there were only a small number of cases of these serotypes [31] . tv003/tv005 is a tetravalent live attenuated vaccine which includes three denv serotypes (denv-1, -3, à4) that have undergone attenuation through direct mutagenesis (a 30 base-pair deletion), while the denv-2 candidate consists of a denv-4-denv-2 chimera. the butantan institute in brazil, which is the sponsor of butantan-dv (tv003), received regulatory approval in december 2015 to begin a phase 3 trial in brasil. three other denv vaccines are in less advanced development. they are an inactivated vaccine, a dna vaccine, and a subunit (the e glycoprotein) vaccine. but the difficulties of developing effective and safe dengue vaccines are multiple, as seen in the cyd-tdv experience, and many issues still remain, including: 1. the vaccine should elicit equal protection against the four denv serotypes, which has been extremely difficult to achieve, in view of competition between strains and/or ade of some strains: the question has been raised of whether it really is a must to develop tetravalent vaccines? 2. whether antibodies are associated with protection or risk (ade) seems to depend on titer, homotypy versus heterotypy, etc. how can that be understood and controlled? 3. why does severity of the disease, especially that of the postvaccination adverse events, vary with age? and 4. what is the feasibility and what will be the cost of a necessary pre-vaccination screening? nevertheless, the substantial public health benefits of even a moderately effective dengue vaccine continue to drive all the efforts at developing dengue vaccines [29, 30] , hoping that safety concerns may be adequately addressed. a large number of zika vaccine candidates are under development and have entered clinical trials, including: a mrna vaccine; a dna vaccine that encodes the zikv prm and e genes and is presently entering phase iib trials in the usa, brazil, and several countries in latin america (puerto rico, mexico, panama, peru, columbia..); a purified inactivated vaccine adjuvanted with alum, which was shown to be immunogenic after two doses by the im route in a phase 1 clinical trial; and a chimeric measles virus vaccine that expresses the prm and e genes of zikv. as outlined by dr anna durbin (john hopkins bloomberg school of public health) many hurdles still remain before licensure of a safe and effective zikv vaccine can occur. the transmission of zikv has declined so much that it will be difficult to perform a phase 3 efficacy study. in addition, clinical trial efficacy endpoints for a zikv vaccine are not well established: one can wonder if a vaccine will not have to fully prevent infection in order to prevent microcephaly, a very high bar for any vaccine indeed! dr georges thiry (sas senergues, france) reported the creation of the 'coalition for epidemic preparadness innovations' (cepi), which was launched in january 2017 in oslo, london and washington with the aim to prevent future epidemics by the development of new vaccines. three major targets have been selected for the manufacturing and testing of candidate vaccines: mers-cov, lassa fever virus and nipah virus. cepi is responsible for vaccine development from preclinical to phase 2a trial. several vaccines are being followed up: a lassa-vsv vaccine, developed by iavi; a lassa-dna vaccine; a lassa-measles (mv) vaccine, developed by themis; a mers-cov-mv vaccine, also developed by themis; and a nipah glycoprotein subunit vaccine with adjuvant. most phase 1 studies have taken place in 2018-19 and phase 2a trials are expected to follow in 2020-22. arboviruses are in the news and at the top of social, political and public health agendas. arbovirus epidemics will increasingly threaten global, national and local political and economic security and create a global public health emergency. not only is there an increased risk of epidemic arboviral diseases in rural areas, but there also is now an increased risk of urban epidemics. dengue epidemics have recently seen their amplitude increase dramatically: in 2019, there were 10 fold more reported cases of denv infection in brazil than during the preceding year, leading to 600 deaths; during the same period, 44,000 dengue-infected persons had to be hospitalized in bangladesh, where some 100 deaths occurred, and more than 1400 deaths from dengue were reported in the philippines! an estimated 390 million dengue infections occur annually [9] . the development of vaccines and vector control tools to prevent arbovirus diseases is actively being pursued [32, 33] , and the possibility of developing a trivalent vaccine against zikv, chikv and wnv is even being entertained. many hurdles however, remain before licensure of a safe and effective zikv vaccine can occur, as outlined above. similarly, the difficulties at developing an effective and safe denv vaccine are multiple, and many questions still arise. what will be the cost of implementing pre-vaccination screening? whom to vaccinate in places where denv seropositivity in 9 years of age turns out to be very low (only 10% in singapore for example)? the dramatic emergence and spread of epidemic arboviral diseases has made it necessary to reassess surveillance strategies. all at-risk countries should have an enhanced passive disease surveillance system based on well-defined case definitions and supported by serological and virological laboratory testing. an active laboratory syndromic surveillance system, such as was developed in the past by who for influenza or for poliomyelitis, is badly needed. it is hoped that such a system will be set up rapidly. but we also need more effective mosquito control tools to use in conjunction with vaccines, timely access to clinical serices and appropriate care. only by using an integrated approach to prevention and control will we be able to successfully reverse the trend of emergent epidemic arboviral diseases. 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 xxth century dengue pandemic dengue and dengue hemorrhagic fever the global threat of emergent/reemergent vector-borne diseases. in: vector-borne diseases: understanding the environmental, human health, and ecological connections epidemic arboviral diseases: priorities fror research and public health increase in reported prevalence of microcephaly in infants born to women living in areas with confirmed zika virus transmission during the first trimester of pregnancy -brazil importation of yellow fever into china: assessing travel patterns the continuing spread of west nile virus in the western hemisphere the emergence of arthropod-borne viral diseases: a global prospective on dengue, chikungunya and zika fevers the global distribution and burden of dengue global strategy for dengue prevention and control community effectiveness of indoor spraying as a dengue vector control method: a systematic review dengue haemorrhagic fever: diagnosis, treatment, prevention and control who immunization, vaccines and biologicals. vaccine position papers efficacy and longterm safety of a dengue vaccine in regions of endemic disease yellow fever epidemiological update identifying global vulnerabilities to urban transmission of yellow fever virus aedes albopictus and the world trade in used tires, 1988-1995: the shape of things to come urbanization and globalization: the unholy trinity of the 21st century the global distribution of the arbovirus vectors aedes aegypti and ae albopictus policy and practice. a guide to aid the selection of diagnostic tests isolation of zika virus from aedes aegypti mosquitoes in malaysia a single mutation in the prm protein of zika virus contributes to fetal microcephaly assessing the epidemiological impact of wolbachia deployment for dengue control using wolbachia for dengue control: insights from modelling the awed trial (applying wolbachia to eliminate dengue) to assess the efficacy of wolbachia-infected mosquito deployments in yogyakarta, indonesia: study protocol for a cluster randomised controlled trial immunogenicity of fractional-dose vaccine during a yellow fever outbreak -final report benefits and risks of the sanofi-pasteur dengue vaccine: modeling optimal deployment dengue vaccine: hypotheses to understand cyd-tdvinduced protection the long-term safety, public health impact, and cost-effectiveness of routine vaccination with a recombinant, live-attenuated dengue vaccine (dengvaxia): a model comparison study effect of serostatus on dengue vaccine safety and efficacy efficacy of a tetravalent dengue vaccine in healthy children and adolescents beyond efficacy: the full public health impact of vaccines estimating the full public health value of vaccination the organizing committee of the meeting included the following scientists: drs duane j gubler, jacques louis, christopher b nelson, mauricio nogueira, valentina picot, usa thisiyakorn, in-kyu yoon, and mrs cindy grasso.moderators and presenters were drs duane gubler, usa thisiyakorn, joao bosco siqueira, mauricio lacerda nogueira, christopher nelson, rome buathong, nikos vasilakis, michael gaunt, patricia brasil, marc lecuit, anna durbin, georges thiry, annelies wilder-smith, louis lambrechts, scott ritchie, in-kyu yoon, and elizabeth hunsperger. key: cord-214822-pfx1eh5b authors: sotolongo-costa, oscar; weberszpil, jos'e; sotolongo-grau, oscar title: a fractal viewpoint to covid-19 infection date: 2020-07-14 journal: nan doi: nan sha: doc_id: 214822 cord_uid: pfx1eh5b one of the central tools to control the covid-19 pandemics is the knowledge of its spreading dynamics. here we develop a fractal model capable of describe this dynamics, in term of daily new cases, and provide quantitative criteria for some predictions. we propose a fractal dynamical model using conformed derivative and fractal time scale. a burr-xii shaped solution of the fractal-like equation is obtained. the model is tested using data from several countries, showing that a single function is able to describe very different shapes of the outbreak. the diverse behavior of the outbreak on those countries is presented and discussed. moreover, a criterion to determine the existence of the pandemic peak and a expression to find the time to reach herd immunity are also obtained. the worldwide pandemic provoked by the sars-cov-2 coronavirus outbreak have attracted the attention of the scientific community due to, among other features, its fast spread. its strong contamination capacity has created a fast growing population of people enduring covid-19, its related disease, and a non small peak of mortality. the temporal evolution of contagion over different countries and worldwide brings up a common dynamic characteristic, in particular, its fast rise to reach a maximum followed by a slow decrease (incidentally, very similar to other epidemic processes) suggesting some kind of relaxation process, which we try to deal with, since relaxation is, essentially, a process where the parameters characterizing a system are altered, followed by a tendency to equilibrium values. in physics, clear examples are, among others, dielectric or mechanical relaxation. in other fields (psychology, economy, etc.) there are also phenomena in which an analogy with "common" relaxation can be established. in relaxation, temporal behavior of parameters is of medular methodological interest. that is why pandemics can be conceived as one in which this behavior is also present. for this reason, we are interested, despite the existence of statistical or dynamical systems method, in the introduction of a phenomenological equation containing parameters that reflect the system s behavior, from which its dynamics emerges. we are interested in studying the daily presented new cases, not the current cases by day. this must be noted to avoid confusion in the interpretation, i.e. we study not the cumulative number of infected patients reported in databases, but its derivative. this relaxation process in this case is, for us, an scenario that, by analogy, will serve to model the dynamics of the pandemics. this is not an ordinary process. due to the concurrence of many factors that make very complex its study, its description must turn out to non classical description. so, we will consider that the dynamics of this pandemic is described by a "fractal" or internal time [1] . the network formed by the people in its daily activity forms a complex field of links very difficult, if not impossible, to describe. however, we can take a simplified model where all the nodes belong to a small world network, but the time of transmission from one node to other differs for each link. so, in order to study this process let us assume that spread occurs in "fractal time" or internal time [1, 2] . this is not a new tool in physics. in refs. [3] [4] [5] this concept has been successfully introduced and here, we keep in mind the possibility of a fractal-like kinetics [6] , but generalizing as a nonlinear kinetic process. here we will follow to what we refer as a "relaxation-like" approach, to model the dynamics of the pandemic and that justify the fractal time. by analogy with relaxation, an anomalous relaxation, we build up a simple nonlinear equation with fractal-time. we also regain the analytical results using a deformed derivative approach, using conformable derivative (cd) [7] . in ref. [8] one of the authors (j.w.) have shown intimate relation of this derivative with complex systems and nonadditive statistical mechanics. this was done without resort to details of any kind of specific entropy definition. our article is outlined as follows: in section 2, we present the fractal model formulated in terms of conformable derivatives, to develop the relevant expressions to adjust data of covid-19. in section 3, we show the results and figures referring to the data fitting along with discussions. in section 4, we finally cast our general conclusions and possible paths for further investigations. let us denote by f (t) the number of contagions up to time t. the cd is defined as [7] d α note that the deformation is placed in the independent variable. for differentiable functions, the cd can be written as an important point to be noticed here is that the deformations affect different functional spaces, depending on the problem under consideration. for the conformable derivative [8] [9] [10] [11] [12] , the deformations are put in the independent variable, which can be a space coordinate, in the case of, e.g, mass position dependent problems, or even time or spacetime variables, for temporal dependent parameter or relativistic problems. since we are dealing with a complex system, a search for a mathematical approach that could take into account some fractality or hidden variables seems to be adequate. this idea is also based in the fact that we do not have full information about the system under study. in this case, deformed derivatives with fractal time seems to be a good option to deal with this kind of system. deformed derivatives, in the context of generalized statistical mechanics are present and connected [8] . there, the authors have also shown that the q − def ormed derivative has also a dual derivative and a q − exponential related function [13] . here, in the case under study, the deformation is considered for the solutions-space or dependent variable, that is, the number f (t) of contagions up to time t. one should also consider that justification for the use of deformed derivatives finds its physical basis on the mapping into the fractal continuum [8, [14] [15] [16] . that is, one considers a mapping from a fractal coarse grained (fractal porous) space, which is essentially discontinuous in the embedding euclidean space, to a continuous one [9] . in our case the fractality lies in the temporal variable. then the cd is with respect to time. a nonlinear relaxation model can be proposed here, again based on a generalization of brouers-sotolongo fractal kinetic model (bsf) [3, 4, 17] , but here represented by a nonlinear equation written in terms of cd: where τ is our "relaxation time" and q and α here are real parameters. we do not impose any limit for the parameters. equation (3) has as a well known solution a function with the shape of burr xii [18] , with : the density (in a similar form of a pdf, but here it is not a pdf) is, then: where ,which can be expressed as: where the parameter are or, in a simpler form for data adjustment purposes with this is very similar, though not equal, to the function proposed by tsallis [19, 20] in an ad hoc way. here, however, a physical representation by the method of analogy is proposed to describe the evolution of the pandemics. though we have introduced a, b, c, b, and a as parameters to simplify the fitting, the true adjustment constants are, clearly, q, τ and α. note that we do not impose any restrictive values to the parameters. there is no need to demand that the solution always converge. the equation to obtain burr xii has to impose restrictions but this is not the case. in burr xii the function was used as a probability distribution. but here the function describes a dynamic, which can be explosive, as will be shown for the curves of brazil and mexico. therefore, if we consider infinite population, a peak will never be reached unless the circumstances change (treatments, vaccines, isolation, etc.). our model does not impose finiteness of the solution. the possibility for a decay of the pandemic in a given region in this model requires the fulfillment of the condition what expresses the property that what means that the function has a local maximum. if this condition is not accomplished, the pandemic does not have a peak and, therefore, the number of cases increases forever in this model. in this case there is, apart from the change of propagation and development conditions, the possibility for a given country that does not satisfies condition (8), to reach "herd immunity", i.e., when the number of contagions has reached about 60% of population, in which case we may calculate the time to reach such state using (4), assuming t 0 = 0: we will work with what we will call t 1000 ahead and that seems to make more sense and bring more information. with eq. (7) let us fit the data of the epidemic worldwide. the data was extracted from johns hopkins university [21] and the website [22] to process the data for several countries. we covered the infected cases taken at jan 22 as day 1, up to june 13. the behavior of new infected cases by day is shown in figure 1 . the fitting was made with gnuplot 5.2. as it seems, the pandemic shows some sort of "plateau", so the present measures of prevention are not able to eliminate the infection propagation in a short term, but it can be seen that condition (8) is weakly fulfilled. table i . condition (8) is satisfied. in the particular case of mexico the fitting is shown in figure 2 . in this case condition (8) is not fulfilled. in terms of our model this means that the peak is not predictable within the present dynamics. something similar occurs with brazil, as shown in figure 3 . the data for brazil neither fulfill the condition (8) . in this case there is neither the prevision of a peak and we can say that the data for mexico and brazil reveals a dynamics where the peak seems to be quite far if it exists. but there are some illustrative cases where the peak is reached. progression of the outbreak in cuba and iceland are shown in figure 4 and 5 respectively. condition (8) is satisfied for both countries and we can see that the curve of infection rate descends at a good speed after past the peak. now let us take a look at united states data, shown in figure 6 . the usa outbreak is characterized by a very fast growth until the peak and, then, very slow decay of the infection rate is evident. as discussed above, the outbreak will be controlled for almost infinite time in this dynamics. there is also some intermediate cases as spain and italy, shown in figures 7 and 8 . in this case the data exhibits the same behavior as in usa, a fast initial growth and a very slow decay after the peak. however, the outbreak is controlled in a finite amount of time. in table i we present the relevant fitting parameters, including herd immunity time, t hi and t 1000 , the time to reach a rate of 1000 infections daily. this, for countries that have not reached the epidemic peak, mexico and brazil. we also include the population, p ; of each country. table i . t hi = 778 days. condition (8) is not satisfied. table i . condition . figure 6 . daily infections in usa, where the peak looks already surpassed. here again, the behavior of the pandemic in this country looks well described by eq. (7). see fitting parameters in table i . condition (8) is satisfied. table i . condition (8) is satisfied. table i but let us briefly comment about herd immunity. those countries that have managed to stop the outbreak, even with relative high mortality as spain and italy, will not reach the herd immunity. as a matter of fact, this can not be calculated for those countries. then, we can see countries like brazil where, if the way of deal with the outbreak do not change, the herd immunity will be reached. even when it seems desirable, the ability to reach the herd immunity brings with it a high payload. that is, for a country like brazil the herd immunity would charge more than 100 million of infected people. that is, much the same as if a non small war devastates the country. there is an alike scenario in mexico, but the difference here is that the value for t hi is so high that sars-cov-2 could even turn into a seasonal virus, at least for some years. we can expect around the same mortality but scattered over a few years. a special observation deserves usa, where t hi tends to infinity. here we can expect a continuous infection rate for a very long time. the outbreak is controlled but not enough to eradicate the virus. virus will not disappear in several years but maybe the healthcare system could manage it. the virus will get endemic, and immunity will never be reached. however the infections and mortality rate associated with it, can be, hypothetically, small if compared with mexico and brazil. we can also compare the speed of the outbreak in different countries. as we already said in table i we calculated t 1000 for some countries. however, it should be noticed that this time is not calculated from day 0, which is always january 22, but for the approximated day when the outbreak began in the correspondent country. by example, in brazil there was no cases at january, 22 but the first cases were detected around march, 10. so both, data fitting and t 1000 , were calculated from march, 10. in this work, for the first time, we presented a model built using the method of analogy, in this case with a nonlinear relaxation-like behavior. with this, a good fitting with the observed behavior of the daily number of cases with time is obtained. the explicit expressions obtained may be used as a tool to approximately forecast the development of the covid-19 pandemic in different countries and worldwide. in principle, this model can be used as a help to elaborate or change actions. this model does not incorporate any particular property of this pandemic, so we think it could be used to study pandemics with different sources. with the collected data of the pandemics at early times, using this model, it can be predicted the possibility of a peak, indefinite growth, time for herd immunity, etc. what seems to be clear from the covid-19 data, the fitting and the values shown in the table i , is that sars-cov-2 is far from being controlled at world level. even when some countries appear to control the outbreak, the virus is still a menace for its health system. furthermore, in the nowadays interconnected world it is impossible for any country to keep closed borders and pay attention to what happens only inside. all isolation measures should be halted at some time and we can expect new outbreaks in countries like spain or herd immunity. indeed, the model made possible to make an approximate forecast of the time to reach the herd immunity. this may be useful in the design of actions and policies about the pandemic. we have introduced the t 1000 , that gives information about the early infection behavior in populous countries. a possible improvement of this model is the formal inclusion of a formulation including the dual conformable derivative [12, 13] . this will be published elsewhere. proceedings of ieee conference on electrical insulation and dielectric phenomena-(ceidp'94 we acknowledge dr. carlos trallero -giner for helpful comments and suggestions the authors declare that they have no conflict of interest. key: cord-329469-vbk42y1l authors: palamim, camila vantini capasso; ortega, manoela marques; marson, fernando augusto lima title: covid-19 in the indigenous population of brazil date: 2020-10-06 journal: j racial ethn health disparities doi: 10.1007/s40615-020-00885-6 sha: doc_id: 329469 cord_uid: vbk42y1l brazil has 896,917 indigenous individuals distributed among 505 indigenous lands. there are 274 different indigenous languages within 305 indigenous ethnic groups. the indigenous population is susceptible to pandemics, especially to the current pandemic of covid-19, which has spread rapidly. in brazil, after the first covid-19-confirmed indigenous case on 05th june 2020, more 420 suspected cases, 1727 confirmed cases being 934 active cases, 715 cases with clinical cure, and 70 cases of death were accounted through the first week of june. the number of cases is underestimated, according to the special secretariat for indigenous health (sesai) database, since the deaths are due to respiratory failure, possibly caused by covid-19, but not confirmed. the first covid-19-caused death was a 15-year-old indigenous yanomami teenage from roraima state without known previous diseases history and/or comorbidities. in the present study, the importance of social isolation, especially for indigenous people who are more vulnerable to the covid-19, was highlighted by the identification of the infection community. an indigenous of the kokama ethnicity was infected after coming in contact with a medical doctor who was infected with the disease. later, it was noticed that both, indigenous and doctor, were responsible for covid-19’s transmission to 43 other indigenous individuals (30 in alto rio solimões and 13 in parintis), causing possibly other confirmed deaths. the impact of covid-19 for indigenous population might be an unprecedented tragedy, and the government in brazil must take emergency measures as the social isolation. coronavirus disease 2019 (covid19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) that was first identified in december 2019 in wuhan, china, and it has spread globally causing a pandemic. according to the world health organization (who), in 05th june 2020, more than 6.8 million cases have been reported across 213 countries and 2 international conveyances and more than~400,000 deaths reported [1, 2] . in brazil, a total of 630,708 cases with 34,625 deaths were described, which occurred in all brazilian states and federal district. the covid-19 pandemic started at a time when brazilian government is seeking to develop the amazon for mining, logging, farming, and reviewing the protected status of the tribal lands. at the same time, malnutrition, hepatitis b, tuberculosis, and diabetes as well as the lack of access to health care could mean that these tribes would be particularly vulnerable to the virus outbreak. indigenous groups are urging intruders, miners, loggers, poachers, drug traffickers, land grabbers, missionaries, and tourists who can be vectors of transmission to expel from their lands outsiders who could introduce the disease, according to the indigenous organizations of the brazilian amazon. indigenous tribes have already seen their communities ravaged by exogenous diseases in the past. during the 2009 h1n1 influenza pandemic, their death rate was 4.5 times higher than the rest of the brazil's general population [3] . moreover, vaccination as management against h1n1 failed to protect an indigenous community in 2016, and hundreds of indians, mainly from guaraní tribe in the south of brazil, have died [4] . presently, respiratory diseases cause approximately one-third of indigenous deaths in brazil, which can be a complicating factor during the covid-19 pandemic. to safeguard the vulnerable indigenous from brazil, the covid-19 data needs to be disaggregated by ethnicity, since the sequence of sars-cov-2 analysis has showed that the genome sequences of the virus from different patients are very conserved [5] . thus, the aim of the present study is to discuss the epidemiologic and social characteristics of indigenous population aiming to protect them from covid-19 pandemic. in 2010, the brazilian institute of geography and statistics (ibge) has conducted the last population census in brazil [6] . in this context, some peculiarities in relation to the indigenous population who live in brazil and the possible devastating effects of covid-19 on this population are described in the present study. the indigenous population has been reported in all brazilian states and federal district. thus, 896,917 (517,383 in indigenous lands and 379,534 in urban areas) indigenous individuals were censured in 2010, in accordance with their traditions, customs, culture, and ancestry. in addition, 505 indigenous lands and territories were described, representing~12.5% of the brazilian territory, which there was a wide variation in the number of indigenous inhabitants per land [6, 7] . thus, six lands presented more than 10,000 indians, 107 presented between more than 1000 and less than 10,000 indians, 291 between more than 100 and less than 1000 indians, and 83 up to 100 indians. the land with the largest indigenous population was yanomami in the amazonas and roraima states with 25,700 indigenous individuals. in brief, table 1 shows the number of inhabitants, number of indigenous individuals by living at indigenous lands or in urban areas, demographic density, and area distributed by brazilian states and federal district. despite the identical gender ratio inside all indigenous population (~50%), indian females are more prevalent in urban areas and indian males in indigenous lands. in the indigenous population, high fertility and mortality rates have been described, which characterizes an age pyramid with a broad base. the indigenous population is currently divided into 305 ethnic groups according to linguistic, cultural, and social affinities (250 on indigenous lands and 300 outside their lands), being the largest one known as tikúna (6.8% of the indigenous population). the ethnicities' concentration in indigenous lands occur from 251 to 500 individuals by community, contrasting with outside indigenous lands that occur from 50 to 10,000 individuals. in relation to cultural diversity, an important marker is the language, which totalizing 274 different ones. the percentage of indigenous population who speak portuguese, the national language of brazil, is extremely variable between ethnic groups. interestingly, 12.6% of the indigenous' homes are known as hollow type called as "oca or maloca," while the rest as "house" type, predominately. in indigenous lands, "ocas" type is also not common, only 2.9% contrasting with 58.7% of "house" type. in addition, 36.1% of indigenous' homes have no bathroom, and in indigenous lands, there are highest sewage deficits with a predominance of the use of the rudimentary cesspool (65.7%). moreover, access to water supply, electricity, and garbage collection was more precarious for individuals living on indigenous lands than in urban areas. among the indigenous population, 52.9% has no income whatsoever and it is observing a greater proportion in indigenous lands (65.7%) compared with urban areas. it is possible also to verify that many jobs are carried out collectively according to their culture. in the indigenous population structure, recreation and work are not easily separable and the relationship with the land is wide broad, not having an association with private property. in brazil, the indigenous community fears the covid-19 pandemic [8] , and although containment measures have been taken, it was not possible to prevent the contagion of the indigenous population. currently, according to the ministry of health by the special secretariat for indigenous health [9] (05th june 2020), among the indigenous population are as follows: (i) 420 suspected cases; (ii) 1737 confirmed cases being 934 active cases; (iii) 715 recovered cases; (iv) and 70 deaths ( table 2 ). the deaths occurred in 18 special indigenous health district (dsei) from a total of 34 dseis, mainly affecting alto do rio solimões (23 deaths), guamá-tocantins (11 cases), and alto rio negro (5 cases). possibly, the data presented does not represent the total number of cases, and it is not updated daily [10] . as historical marks for covid-19 in brazil and its prevalence in the indigenous population, we have: the doctor has consulted ten patients before the covid-10 diagnosis. after these period of time corresponding to the first month after the first case of covid-19 among indigenous [9, 10] , a total of 70 indigenous deaths were described in 05th june 2020. the deaths occurred mainly among older indigenous or with comorbidities. the indians are the natural holders of the lands that make up the brazilian territory. however, during the colonization, there was a drastic reduction of the indigenous population. in the colonization period, indigenous totalized~2 millions of inhabitants. in the current context, there is~75% reduction in that number, in part due to the pandemic cycles that played a role. the indigenous people do not form a single social and cultural structure, but rather a socially and culturally diverse group, which can be evidenced by the number of languages among different ethnicities. the loss of indigenous ethnicities, in addition to characterizing the loss of life, reflects cultural and social loss that are irreparable. it is possible to determine the route of sars-cov-2 in the presented indigenous cases, mainly in the dsei alto rio solimões -amazonas. the first case had previous contact with a doctor who, in the latency phase, had access to an indigenous group, and among them, an indigenous woman was infected. when the indigenous woman returned to her ethnic group, she spreads the virus, and after~1 month, numerous cases occurred among the members of her ethnic group. indigenous characteristics are important to describe and, among them, the fundamental role of older individuals. senior individuals represent the knowledge and culture of the indigenous population. however, some traditional culture habits have been mixed with modern society habits. covid-19 is associated with a higher risk of death in older patients and comorbidities. evaluating the indigenous cases described here, the age ranged from 0 months to 88 years, being one of the oldest an indigenous leader and an invaluable loss for their indigenous ethnic group. still, among the cases, many indigenous presented comorbidities associated with a greater severity of covid-19. the impact of covid-19 pandemic on tribal chief (cacique) or village elder can lead to the extinction of their cultures, because the traditions are passed on orally by the elders [11] . at the time of the pandemic, it is important to minimize contact with indigenous groups to limit the contagion, which is a crucial measure to be taken [8] . however, in addition to the indigenous socialization outside their lands, especially in the southeast region, they have contact with health professionals and other individuals as loggers, miners, and squatters, who often trespass on the indigenous lands and have taken advantage of the covid-19 pandemic to optimize their profiteering in areas previously preserved and destined to indigenous people by law. despite the social struggles to minimize the devastation of the forest and reduce the proliferation of infectious diseases [12, 13] , the current brazilian political scenario did not create a protective environment and deforestation has increased exponentially [14] . as described by ferrante and fearnside (2020) , the indigenous community should be considered as a risk group, especially if considering the impact that other pandemics have had on this population, forcing the governmental actions as to highlight the isolation and protectionism position [15] . however, as described by the authors, the brazilian authorities are trying to minimize the possibly catastrophic effect of covid-19 pandemic for the indigenous group. however, it is crucial to understand the effects of territorial invasions in the covid-19 pandemic, mainly as a risk factor to promote the infection by sars-cov-2 [16] . an important factor is to obtain the epidemiological data regarding ethnicity, such as caucasoid or negroid, and the application of the same data to understand the progression of the disease in communities such as indigenous population [17] . regardless of life quality on indigenous territories as other regions, brazil have low rates of access to drinking water and basic sanitation, both of which can optimize the progression of the covid-19 virus. another important fact is that in the northern region, where there are the largest number of indigenous population mainly in the state of amazonas, 100% of the beds in the intensive care units were already occupied [11] . thus, there was a health service collapse due to covid-19 pandemic [11] . besides, death numbers due to the respiratory illnesses exceeded the expected values for the time of the year compared with previous years. finally, the limited access of indigenous population to health services are often dependent on doctors and other health professionals visiting their lands. possibly, many indigenous individuals who had contact with the first cases will die and will not be statistical counted due to the lack of knowledge about the disease and the possibility of its diagnosis. in the current scenario, it is difficult to have hope and believe that all brazilians with covid-19 will have the ideal medical support and recommended by the world health organization. probably, many brazilians have died and will die from covid-19 without proper diagnosis and/or management. in the indigenous population, the scenario can be even more tragic, since, unfortunately, it is a covid-19 vulnerable and at-risk population. historically, indigenous population has been devalued and discriminated against by the federal government. politics [18] and technical support [19] , mainly associated with the diagnosis, should be better implemented in brazil to provide support to all individual during the pandemic, mainly the more vulnerable to covid-19. in conclusion, our data reveal the importance of social isolation, especially for indigenous population that were described as vulnerable and at-risk for covid-19, highlighted by the identification of community infection. an individual of the kokama ethnicity was infected after contact with a doctor with the disease, and both, the indigenous and doctor, were responsible for transmitting the disease to other indigenous in the alto rio solimões and in parintis, causing some of the confirmed deaths. the impact of covid-19 may be an unprecedented tragedy for the indigenous population, and the brazilian government must take emergency measures to encounter the tragic outcomes of the disease. author contributions all authors have approved the manuscript and agreed with its submission to the journal. also, cvcp, mmo and falm wrote and revised the manuscript. pandemic h1n1 influenza and indigenous populations of the americas and the pacific investigation of an outbreak of acute respiratory disease in an indigenous village in brazil: contribution of influenza a(h1n1)pdm09 and human respiratory syncytial viruses genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding características da população e dos domicílios: resultados do universo. rio de janeiro: ibge nacional do índio. www.funai.gov.br. accessed at 03 rd indigenous communities in brazil fear pandemic's impact articulation of the indigenous peoples of brazil brazil's policies condemn amazonia to a second wave of covid-19 beyond diversity loss and climate change: impacts of amazon deforestation on infectious diseases and public health deforestation and brazil's indigenous population bolsonaro threatens survival of brazil's indigenous population protect indigenous peoples from covid-19 brazil threatens indigenous lands covid-19: review indigenous peoples' data covid-19 in brazil one million cases of covid-19: what have we learned publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations conflict of interest the authors declare that they have no conflict of interest. key: cord-032786-ps2mtin4 authors: py, fábio title: bolsonaro’s brazilian christofascism during the easter period plagued by covid-19 date: 2020-09-28 journal: int j lat am relig doi: 10.1007/s41603-020-00120-4 sha: doc_id: 32786 cord_uid: ps2mtin4 the article highlights the media actions of the president of brazil, jair bolsonaro, in the face of the expansion of the pandemic of the new coronavirus, covid-19, in brazil. for this, the easter week of 2020 was separated when a comparative operation of bolsonaro with the figure of jesus christ, in his social networks—a tip of what we call brazilian christofascism—was woven. thus, precisely in the period of the celebration of the death and resurrection of the christian messiah, we sought to connect bolsonaro with the figure of jesus, placing him as the country’s savior in the posts on his social networks. for this demonstration we assume that each post would be a “scene,” which are “politically staged dramatic acts” (rancière), in this case, media scenes. therefore, we argue that during the period, the intellectuals of the bolsonaro government designed seven scenes to readjust the presidential figure to christianity for its loss of popularity for the public defense of vertical isolation. the present essay aims to discuss the intentional use, by the president of the republic of brazil, jair messias bolsonaro, and his "intellectuals" (gramsci 1982; py and pedlowski 2018) , of the figure of the messiah with more direct likeness to the historic narrative of jesus christ in the easter of 2020. the hypothesis goes by a centralized version of political theology being developed precisely in the easter period of 2020, due to bolsonaro's forfeiture of popular support due to his relativizing posture on the positive effects of the quarantine imposed as a response to the covid-19 pandemic. 1 hence, there was a 7% satisfaction index loss regarding may 2020 in the government's assessment through. trend changes were due to the way he behaved before the coronavirus pandemic, covid-19. his stance went on the opposite way compared with the other national leaders (governors and parliamentarians) in the face of the spread of the disease, which is explicited below by "xp investimentos" graphic. evaluation framework of the temer and bolsonaro governments from may 2010 to april 2020 source xp investments brasil, april 2020. seeking to reverse the popularity loss, the government's "intellectuals" (gramsci 1982) counter-produced an imaginary discourse, placing him as a "good christian" (getsemani 2020), nurtured by messianic appeal, in order to readjust his conservative and fundamentalist christian social base-which was being drained its political support. bolsonaro fed his social base and reinforced with a sort of manichaeism idealpromoting this "war of the gods" (lowy 2000) -and doing so he assumes himself as president of the christians (bolsonaro 2020a; bolsonaro 2020b ) and brings to bear a simplification of political conflicts, which started to constitute clashes between "good versus evil." in this arrangement, the conflict occurs between those who represent evil, in the caricature of "communists" or "pt members" (leftist political party), and "citizens of good" (py 2019; . hence, the present article highlights bolsonaro's intellectuals mechanism when they bet on the resumption of popular support, as they have already used in july 2019, when "they associate the image of bolsonaro with the figure of jesus christ, in the middle of a serious government crisis" (py 2019) . by doing so, he recounted the figure of the messiah jesus christ into the trajectory of bolsonaro, a method exercised by the president's intellectual groups, as already written in the article "bolsonaro's christofascist christology" (py 2019) . however, in the week of easter 2020, this resource was reused under the excuse of the religious celebration of christ's death and resurrection. the allegory of the christian easter was the pretext of building the via crucis bolsonarista, as a suffering servant who overcame death for the defense of the nation. addressing the work of carl schmitt (1988), we may derive the strength of the christian appeal by understanding it as a media strategy to keep the authoritarian government. the political operation of religious use further legitimizes authoritarianism in brazil, here addressed as "brazilian christofascism." the fact constitutes itself as bolsonarism (almeida 2019) fabricates an endless "war of the gods" as a strategy to shape a theology of power sustained in the memory of the colonizing european christ (dussel 2012) . therefore, in the midst of easter 2020, under the covid-19 pandemic context, bolsonaro government developed an offensive by redesigning an authoritarian christology of power based on the figure of martyr and messiah, equating it to the memory of jesus christ easter. an orchestrated action in early april, when a national fast for palm sunday (april 5, 2020) was called for, intensified during the week, reaching its peak on easter sunday (april 12, 2020). precisely on the day that christians celebrate christ's resurrection and victory over death, in which it was solely compared, by the president, to the stabbing fact he suffered in the 2018 electoral year process. consequently, we have set apart seven "orchestrated scenes" (rancière 2012 ) by the president's body of intellectuals, collected from the social media network instagram that culminated in the construction of the bolsonaro's "paschal" myth. it is assumed that the concept of "scene" comes from jacques rancière's book, la méthode de l'egalite (rancière 2012) , when it indicates that it is "a convergence between theory and practice when capturing the application of the makeup of the elements , the construction of figures, messages, and imagery, printing an exercise, a practice" (rancière 2012) . by saying out these initial elements, it is appropriate to describe in most details what may define, in brazil, as brazilian christofascism-based on the christofascism of the theologian solle (1970) . thus, we proceed to describe a little about the term and its effects in brazil. featuring the architecture of a messiah given by bolsonaro's governmental leadership, i highlight some conceptual elements that i call "brazilian christofascism." the christofascism of bolsonarist management is promoted in the context of an "authoritarian political theology" (schmitt 1988), based in the apocalyptic environment of coronavirus, based in the "hatred of democratic plurality" (rancière 2014) . his hatred is voiced in the government's techniques to promote discrimination and, mainly, by discriminatory stances and attitudes towards the "heterodox" sectors (bolsonaro 2020a; bolsonaro 2020b) . this was seen in the expansion of the coronavirus in brazil that amplified his habitual anti-democratic appeal of economic breath that justifies the "death policy" ("necropolitica"; mbembe 2014; butler 2020)-against the poorest population, the oldest, the diabetics, and the hypertensive patients (bolsonaro 2020a (bolsonaro , 2020b . the term "brazilian christofascism" is based on the german theologian's own reflections solle (1970) , who created the expression "christofascism" out of a recollection from german nazism, especially about auschwitz, inside her book: beyond mere obedience: reflections on christian ethic for the future (1970). sölle's term is concerned with pointing out "the relations of members of the nationalsozialistische deutsche arbeiterpartei (nsdap -the nazi party) within christian churches in the development of the state" (solle 1970) of german exception. dorothee sölle recalls that the nazi government made use of christian associations and terminology for its social cohesion, therefore bolsonaro government as well. 2 hitler used christian idiom placed in his speeches as the "you know the truth and the truth will set you free" (john 8.32) and "created god, man in his image; in the image of god he created him; man and woman created" -in order to defend the traditional views on german christian family. the führer made crusades into christian gatherings (lutherans, catholics, and confessionals), relating to pastors and priestsamong some lutherans pastors stood out walter hoff, rudolf kittel, and prospt ernst szymanowski, developers of the so-called positive christianity (solle 1970) . in her book, solle (1970) points out that white extremists in the usa would have the same "attitude of hatred, prejudice and racism" previously seen in the imperial nazi regime. when describing fundamentalist groups on american soil, she uses the term "christofascism" as the action of white supremacist groups in the usa, having very little connection with the formation of the state. she was not concerned with the details of the term, hence highlighting an authoritarian political theology of state trends. she points to christofascism as a "blind obedience" when "in relations with the divine of people under authoritarian regimes or within fundamentalist groups" (solle 1970) . solle (1970) considers the "deepening of the unilateral understanding of christianity (...) in the second world war and in the americans in the context of the extremist violence of christian fundamentalists." hence, for her, christofascism is an authoritarian, arrogant, totalitarian, imperialist theology, characteristic "of the church in germany under nazism, and still alive at the end of the 20th century in the white extremist groups" (solle 1970 ) of the usa. with the expression, she considers it to be a "deviation from fundamentalist christianity in the service of white and patriarchal supremacism, which extends through the spread of fear, punches, misogyny and structural racism" (solle 1970) . therefore, affected by the strength of the idea, it is believed that in south america, another type of christofascism was developed: "the brazilian" type (py 2019) . it is a mixture of both extremist christian (fundamentalist) groups as it is an authoritarian, despotical, form of government, such as bolsonaro's. in this sense, one is more concerned with bolsonaro's "architecture of government power" (schmitt 1988), than with the uses given by the german theologian. sölle does not dwell on "governmental theology" and, even less, on the oppressive theology linked to "coloniality" as dussel (2012) , nor is it inspired by walter benjamin's notion of fascism (2012 and 1940). thus, for benjamin (2012) , the barbarism of authoritarian fascination does not represent a stage of "civilizational regression, but is contained in the very conditions of reproduction of liberal-bourgeois civilization" (lowy 2000) . he understands fascism as political machinery for constituting the "state of exception," part of the migration of governmental techniques that dominated the colonies applied years later in europe. fascism is then understood as a "liberation of the destructive forces produced by a bourgeois civilization in crisis in order to keep the process of accumulation in order" (benjamin 2012) . the libertarian philosopher understands that the wonders imposed by the authoritarian government fits together with conservative conceptions of morality, family, and progress, to engender the transformation of the whole national concept into a "state of effective exception" (gagnebin 2014) . fascist government management involves "disciplining the proletarianized masses, thereby preventing any disturbance to the property regime. it is a matter of allowing such masses to express themselves as masses, as long as the order put is not put in check and that any claims that touch the social structure are contained" (benjamin 2012) . another side face of fascism already pointed out is the legacy of coloniality (benjamin 2012; dussel 2012; cesaire 2010) . when fascism expanded the warlike dimension of capitalism or, at least, increased the war policy of the state to the heterodox people, to the poor (gagnebin 2014) . it is said that the authoritarian form of bolsonarism is projected from christian fundamentalism, by which it simplifies the notion of family in order to promote the elimination of its opponents and/or undesirables, in this case, in the context of covid-19, those who do not fit into the healthy gap range. another trend goes back to the notion of fascism assumed in the material on which brazilian christofascism is laid, the "war of the gods", a term by michael lowy (2000) re-addressing the book science as a vocation by max weber (1998) . for lowy (2000), the conflicts over "the polytheism of values and the insoluble conflict of the basic beliefs gods in modern society." thus, he signals that the term: first (...) it refers to the conflict in the religious field between radically opposed conceptions of god: from the progressive christians and that of conservative christians (both catholic and protestant) -a 'coalition of values' (werkollissionanother weberian term) that , in extreme situations such as that of latin america in the 1980s, it may even be transformed into a civil war. (lowy 2000) the author conceives that in latin american societies, "a real war of gods" takes place, between "various conceptions of gods as a symptom of the social struggles between civil societies and states" (lowy 2000) . we affirm that bolsonarism operates a "war of the gods," sometimes simplifying and sometimes projecting a fascination of the presidential figure with the messianism of christianity. this operation is very well constructed by the "body of intellectuals" (gramsci 1982 ) that draws the presidential figure as a political messiah. whether pointing as a suffering servant, as an anointed one, or as the nation's elect in the context of the covid-19 pandemic in brazil. a last detail cannot be dismissed. brazilian christofascism has been influencing the southern territories, as for example, more recently, new authoritarian modulations have been built in bolivia. we quote the conservative christian coalition that has the figure of jeanine añez, a current interim president, in which in the face of a coup, she has affirmed that the bolivian "bible has returned to the palace." we are not going to stop here in this phenomenon; however, we would like to highlight that there is the growth of other authoritarian governments in the south america, evoking christian discourses, for the implementation of ultraliberal agendas, which would be a circuit of "southern christofascisms." now, after the most theoretical signs, let us move on to the description of the "scene" (rancière 2012 ) built over at easter with the figure of bolsonaro. in order to address the construction of bolsonaro's paschal myth, some "architectural and staged" scenes (rancière 2012) are analyzed by his intellectuals and the president himself to link him to the figure of messiah, savior. it is argued that this practice was done aiming an imaginary passage in which it could be seen on social networks, on the president's instagram (bolsonaro 2020a) . in this arena, he orchestrates videos, photos, and montages that feed daily with a focus on the social media base. then, the focus of analysis took place between the eve of palm sunday, april 5, until easter sunday, april 12, 2020. effectively, it is believed that each "scene" that will be highlighted "contains a series of intentional intents that aim to capture a time in favor of a social practice" (rancière 2012 ) that affect both individually and jointly to build theological content on the figure of the president. with the media operation on the social network, we seek to stylize the image of bolsonaro as messiah of the brazilian nation-a savior also in the context of the covid-19 pandemic. the scene was woven (rancière 2012 ) in a video, with a little more than 4 min on the youtube channel of the getsemani baptist church (igreja batista getsêmani 2020), by the title "outcry and fast for brazil -april 5th -summoning of the president jair messias bolsonaro" to call the population to #jejumpelobrasil, scheduled for april 5, 2020, and posted on the presidential instagram (bolsonaro 2020a) . 3 the call video begins with the verse of 2 chronicles 20, 3: "jehoshaphat decided to consult the lord and proclaimed a fast throughout the kingdom of judah" (baptist church getsemani 2020). after the instance, bolsonaro says "thank you all very much, and those who have faith and believe, sunday is the day of fasting." with the phrasal sentence, bolsonaro does not take 10 s, and the rest of the video is arranged with the biblical texts of 2 chronicles, and the appeal of the evangelical and catholic leaders listed below: r. r soares, andré valadão, rene toledo, silas câmara, abner ferreira, juanribe palharine, abe huber, mario de oliveira, jorge linhares, jose wellington junior, marcos feliciano, rene terra nova, edir macedo, roberto lucena, samuel ferreira, robson rodovalho, valdomiro santiago, hernandes dias lopes, luiz herminio, santanna, roberto brasileiro, elizete rodrigues, marcio valadão, guilherme batista, valdomiro ferreira, humberto vieira, andré fernandes, estevão hernandes, silas malafaia, and samuel câmara (igreja batista getsemani 2020). after the religious leaders sayings, close to the end of the video shooting, he quotes the text of 2 chronicles 7:14: "if my people, who are called by my name, humble themselves, and pray, and seek my face and convert from bad ways, then i will hear from heaven, and forgive your sins, and heal your land" (getsemani baptist church, 2020). in the making of the shooting production, the objective was to address christians that palm sunday should be made a fast day "so god could free brazil from the plague of covid-19" (igreja batista getsêmani 2020). but palm sunday is a more strongly roman catholic tradition for keeping the sunday before easter, recalling jesus' entry into jerusalem over the donkey in the rite. at the video, bolsonaro in a few words summons the christian population to fast, and then another biblical text appears in response saying: "do not be afraid, nor be frightened because of this great crowd; because the battle is not yours, but god's" (v.15; getsemani baptist church 2020). following the sequence of images, with the music and messages in it, it is indicated that it is the king (the ruler) who has to put himself next to god, just like jeosafá (getsemani 2020), because the battle would not be for men and women, but for the divine. in the video, some leaders even claim that the president "would have been anointed to take over the nation" (igreja batista getsêmani 2020). in this first shooting scene, the apostle valdomiro santiago summarizes the date as follows: "praying for the nation, praying for the people, praying for the lord president, that god will sustain him" (igreja batista getsêmani 2020). another leader, silas malafaia, states that "after that, there will be a time of prosperity for brazil that never was seen, and that all catastrophic predictions are annihilated in the name of jesus" (igreja batista getsêmani 2020). the video has the thrust to ennoble a devotion, to mobilize christian sectors to altogether endures the fight against the coronavirus, "to pray and fast so that the plague that plagues the earth" will survive (getsemani 2020), alongside president bolsonaro who is the leader, anointed king to rule the nation. the second scene has taken place on wednesday, april 8, at the exiting of the government headquarters called palácio da alvorada (bolsonaro 2020a) . the president received an expedition of catholics with the image of our lady of fatima. the pilgrims said: "we brought the image of our lady of fatima, because it will free brazil from communism. because all of these mistakes are condemned by us, the roman apostolic catholics" (bolsonaro 2020a) . in this case, bolsonaro's supporters build the narrative, linking nossa senhora de fátima to the fight against communism, inducing that a "cultural war" is taking place (lowy 2000) in brazil, which puts catholicism versus communism. just in front of bolsonaro, the leader of the caravan says "that communism is a mistake and puts catholicism in another direction" (bolsonaro 2020a) . thus, the leader marks his position of contempt for the social tendencies of catholicism, such as liberation theology (lowy 2000) . following the dialog, bolsonaro continues talking to another member of the caravan: president, we also ask that our lady pour out her blessings on you. there's a lot of burden on you right now. you represent this struggle, it is the struggle against communism in our country, that is why we pray for you and we want to pray an ave maria asking for her blessings, which will give you strength. what energy to carry brazil on your shoulders, count on us with our prayers, the victory is ours! (bolsonaro 2020a) in the affirmation, the believer follows the line of "cultural war, which slips into the gods" (lowy 2000) , saying that the spiritual battle that is ongoing in brazil, under covid-19, resembles struggles that face together with enemies of the nation, that is, "the communists" (bolsonaro 2020a) . and, in the last sentence of the dialog, catholics in the motorcade indicate the president as a person separated by the divine: "the lord was raised up by god, he was anointed by god, to be taking our country right now" (bolsonaro 2020a) . for roman catholics, bolsonaro is considered an "anointed" (bloch 1995) and also symbolizes the fight against communism in brazil (py 2020). thus, the group of drivers suggest that bolsonaro has both a political position in which he currently occupies, as well as a religious one, being someone separated by the divine (bolsonaro 2020a) . in the reading of religious, bolsonaro is a mixture of "someone separated by god" (bolsonaro 2020a ) and the symbol of the struggle against communism, such as "means the figure of nossa senhora de fátima" (bolsonaro 2020a) . on the very same wednesday, april 8, 2020, another scene was built by scholars from bolsonarism (almeida 2019). around 8:30 pm, the president made a statement to the nation about the actions he is taking in the face of the pandemic (bolsonaro 2020b). in the speech scene, he says that the country is experiencing a "unique moment in history, and to be president is to look at the whole and not just the parts" (bolsonaro 2020b). thus, he highlights his concerns with the issue of unemployment and isolation due to the covid-19 pandemic. however, just before going on with his speech, he indicates "solidarity with families in the face of this war that we are facing" (bolsonaro 2020b) . even externing solidarity in his speech, he elicits the idea of war that is paramount for his management that in case feeds on conflicts and armed intrigues . he affirms his responsibility to decide the "destiny of the nation in an outbound way, using the team of ministers" (bolsonaro 2020b ) that he has chosen. however, he is moved by the authoritarian moto when he says: "everyone (ministers) must be in tune with me" (bolsonaro 2020b). bolsonaro demonstrates his centralized management tendency, making clear the problems of conducting policies that he had been developing with his former brazilian minister of health, luiz henrique mandetta. the former minister was being controversial, insisting on horizontal isolation while the president affirmed his preference for vertical isolation, that is, only for the elderly (bolsonaro 2020b) . without mentioning names in the speech, he stresses that the minister should be in tune with him, that is, assuming isolation only for the older age group of the population (bolsonaro 2020b) . since the very beginning of the coronavirus pandemic in brazil, bolsonaro has contradicted the sayings of the world health organization (who) regarding the option for isolation . the president justified his reasoning by building a dangerous eugenic dichotomy (butler 2020), like this: "two problems to solve: the virus and unemployment." for him, these two issues should be dealt with simultaneously (bolsonaro 2020b) , that is, the workers, although in pandemic scenario, should leave home and expose themselves to contamination, which may increase the deaths between him and his family (bolsonaro 2020b) . under the false dichotomy "the virus or unemployment" (bolsonaro 2020b), he exposes his necropolitical stance of "delivering parts of the population to death" (mbembe 2014). at the end of the speech, as a christofascist governor, he returns to the christian tone: "i want to deliver a much better country that you received from our successor. let us follow john 8.32: and you will know the truth, and the truth will set you free." now, after building his speech based on the eugenic dichotomy of "the virus or unemployment", bolsonaro (2020b) clings to the christian covering speech to sensitize his catholic and evangelical social base. he quotes his own sayings since 2018 elections (py 2019; py 2020), seeking to fill the political process with biblical colors, in addition to insisting on building a christian government contrary to the other religions that make up the territory (py 2019). in the last words of the video, he says "i wish you all a good friday of reflection and a happy easter sunday! god bless our brazil!". thus, at the end of the scene, he indicates to know the religious temporality of easter week; therefore, with this, he aims to make himself a "good christian" (py 2020). passing the "makeup scenes" (rancière 2012) on wednesday (bolsonaro 2020a; bolsonaro 2020b), on april 8, 2020, the president was silent on social networks almost every thursday without speaking. he remained silent precisely on passion friday, reaffirming that he is familiar with the christian calendar, when it is a "day of silence related, above all to contrition" (boff 1972). passion friday is a specific time in christianity that "symbolizes the day of christ's death, so it is a day for reflection, for the evaluation of each religious" (boff 1972) . even so, it is common for each religious person, at the end of the day, to pronounce himself in "a tone of assessment in relation to the divinity, such as a public declaration of faith before the symbol of the day of death" (boff 1972) of his divinity. good friday is a temporal mark in worldly christianity, symbolizing the day of death of the saving messiah jesus christ. in this context, the president posted, on his profile on social networks, another scene: a biblical text and the image of jesus crucified ( fig. 1; bolsonaro 2020a) . after the day of silence, assuming the process of reflection and evaluation indicated in the christian tradition, bolsonaro posted the fourth media "scenic scene" in easter week, in the early evening. he posted a strong image for christianity, with jesus christ crucified on the cross (bolsonaro 2020a) . alongside the expressive image, the architect attached the fragment of 1 peter 2:24: "he himself carried our sins on the tree in his body, so that we died for sins and lived for justice, for your wounds you have been cured" (bolsonaro 2020a) . now, by that, bolsonaro and his body of intellectuals show that they know other biblical verses, not only the one so quoted john 8:32. the verse of 1 peter 2:24 deals with the question of the mystery of the resurrection. an important verse in which he highlights the idea of "salvation" from christ (boff 1972) . the scholars of bolsonarism (gramsci 1982; almeida 2019 ) make up with the verse of paul, the central apostle of christianity. this verse is written on the walls of several churches in brazil (mendonça 2008), emphasizing the importance of "the coming of christ on earth" (boff 1972) . with the presidential orchestration, he points out that he knows the meaning of jesus' attitude in the death of the cross. in this sense, bolsonaro demonstrates that as a "good christian" (py 2019) , he knows details about the "history of christian salvation" (boff 1972), connecting directly with "his described catholic and evangelical conversational audience" (almeida 2019). after the reflective scene, on good friday, on saturday 11th, at night time, he posted a dramatized video (rancière 2012; bolsonaro 2020a) , telling his story since he took the stab in the electoral process. in the video, he builds his life story from the moment of the stab, in his speech at the thanksgiving service promoted by the evangelical parliamentary front (frente parlamentar evangélica), on december 17, 2019, at planalto palace (bolsonaro 2020a) . in an emotional bias, he talks about the stabbing drama he suffered like this "in the most difficult moment of my life, i just asked god not to leave my seven-year-old daughter an orphan. the rest with friends, with real brazilians, and with god at heart, we will overcome obstacles" (bolsonaro 2020a) . the video commences assuming the condition of a suffering servant, one who fights to live and to defend the brazilian nation. the suffering servant tradition has broad bases in the messianism of the biblical traditions of the hebrew bible, which deals with the "suffering servant" (in the book of the prophet isaiah). they who speak of the "suffering servant, a messiah who in the middle of his mission will be spat out, cut, bruised, who takes the people's pains. the messiah passes through the world to suffer, in order to rescue the people, save them from the bad ways" (schwantes 2008). from the jewish background, the christian mentality is arranged, which internalizes the idea of suffering, struggling messiah, who suffers to "conquer the world and save humanity" (schwantes 2008). for milton schwantes, christian messianic salvation "necessarily goes through the process of struggles, suffering" (2008). so, for bolsonaro's theological intellectuals, linked to christian fundamentalism, bolsonaro's struggle was won by the suffering, grapple, not to "leave his daughter" (bolsonaro, 2020) orphan. by that, bolsonaro reinforces the value of being a father, therefore prioritizing the family, as a universal value for conservative evangelical movements (almeida 2019). bolsonaro affirms that the strength to overcome the attack he has suffered would come from the family or, rather, from his idealization of the christian family. after summoning his family, he says that "with friends", and also, "with real brazilians, with god inside the heart" (bolsonaro 2020a), that he was sure he would overcome everything. thus, this political messiah reissues the patriotism of the military dictatorship, surrounding himself with people who have god-therefore, those who are not in this program are outside their idealization of nation. in that order, directly, he quotes the updated ideas for his governance of "family, homeland and god" (fico 2004), which give strength and confidence to "revive" (bolsonaro 2020a). in part, it turns to the religious tone, related to the family appeal, the patriotic appeal, and the "good christian" appeal in the face of the martyrdom that passed during the elections (py 2019) . following in the "blended scene" (rancière 2012), by video excerpts, he speaks with the verses of the gospel music in the background. the lyrics of the song appealingly say "story of my life, i fought, i suffered, there were times i got it right, others i missed, life is a journey of love and suffering, and the lord accompanied me all the time. he was there when the world came crashing down on me. many said it was the end, i struggled with my faith. through the valley of the shadow of death, the lord made me stronger and that is the story of life. i fought, i suffered" (bolsonaro 2020b) . the song follows what bolsonaro said of his "reviving, of having come out of death" (bolsonaro 2020b) , lumping bolsonaro's trajectory, which is shot in the video at the moment of the stab, going through his recovery at the hospital, the prayers and election (bolsonaro 2020b) . when he reached the end, he showed himself as an exemplary christian figure in the church, praying and kneeling (figs. 2 and 3). thus, his path begins to be drawn, not only as a "good christian," but as a suffering servant and political messiah, his victory is expressed "by the miracle of the presidential sash" (bolsonaro 2020b; . in the video, he says that it was only possible because "god preserved his life" (bolsonaro 2020b ). therefore, due to this ordeal, i would be sent by god to brazil, pointed in the text: "i lay down and slept. i woke up because the lord supported me" (psalm 3:5). therefore, with this fifth scene, in the middle of hallelujah saturday, bolsonaro and his intellectuals present him both as a "good christian" (who goes to church, defends the christian family and the homeland), who begins to draw himself as a leader who has gone through this to be sent, anointed by god to save the nation in the context of covid-19 (py 2019) . amidst hallelujah saturday, or holy saturday, as the temporality of "a time when the hope of jesus' resurrection is celebrated, when after the crucifixion, the disciples project the possibility of resurrection, of reviving" (boff 1972), begins to be appointed as the nation's political-religious messiah. therefore, in this forced exercise of bolsonarist intelligence (gramsci 1982) , emerging from the christian tradition, it shows bolsonaro as someone that jesus is aside, caring for and doing miracles and wonders and so, as shown in figure (3) , of himself being surgically operated with jesus by his side. and for this same reason, a political messiah is made to take care of the nation in these complex and pandemic days. on this further occasion, the sixth scene was made up in bolsonaro's post on the social network during easter sunday morning, april 4, 2020 (fig. 4; bolsonaro 2020a ). in the morning of easter sunday, when the christian celebration that marks the "resurrection of jesus christ, messiah savior, his victory over the roman death empire" opens (boff 1972), bolsonaro makes up a text that deals with of the "nature of christ", that is, within the christian tradition that marks the debate of "jesus, whether he was man or god, or both" (boff 1972) . he makes use of the biblical text in order to publicly demonstrate his faith (mendonça 2008), based on the classic text of the gospel of john: "because god loved the world in such a way that he gave his only begotten son, so that everyone who in him he believes does not perish, but has eternal life" (john 3:16). again, it evokes the gospel of john, the most important book of the bible for the expansion of christianity. john is the most famous gospel among brazilian christians and has its words and fragments "widely used by missionaries and fundamentalist pastors in their pastoral practice in the history of brazil" (mendonça 2008; and also py 2020; zwetsch 2015) . therefore, the gospel of john is the scene of a variation of "theological reasoning for the propagation of the evangelical faith from its message more linked to the greek empire, then to hellenism" (mendonça 2008). by the "scene composition" or configuration (rancière 2012) in the easter post (bolsonaro 2020a) , he affirms the key theme of the day: "he is risen." again, he demonstrates that he has intimacy with the holy scriptures and is thus in tune with the majority tendency of brazilian christianity. this is important to be addressed: with the set of posts, bolsonaro is drawn as an authentic christian of the great evangelical corporations, and his intellectuals (gramsci 1982) operate this makeup in a very well treated manner . (bolsonaro 2020a) with this set of sequential scenes, it aims to demonstrate that the president knows a range of biblical texts and christian themes, not only the so-called "you know the truth and the truth will set you free." at the same time, the scene indicates that he is aware of the "christian salvation theology expressed in the book of john" (zwetsch 2008) and the theological discussion on the "nature of christ" based on this gospel (mendonça 2008) . through this scene, he highlights his knowledge of more elements of christianity for those who doubt his adherence to religion. as the second scene, built on easter sunday, has taken place in the afternoon, at the meeting promoted on the internet (tvbrasilgov 2020) (tvbrasilgov 2020) . at the beginning of the last scene of easter week, bolsonaro opens the video saying "the forty leaders who will transmit a word of faith and hope, and of the meaning of easter" (tvbrasilgov 2020). it strengthens the number and importance of leaders in the religious environment and also reports that a pastor sent him a video and that video was the "most important video he was sending" (tvbrasilgov 2020). he says that the pastor recorded the video from israel, indicating that "jesus' tomb was empty, saying that he was resurrected and went to heaven" (tvbrasilgov 2020). now, with his usual difficulties in articulation, he signals that he knows a little more about the story of jesus from the gospels, who was searched for in the tomb and was not found (boff 1972). the president then has taken the opportunity to say that the event "will comfort everyone who is connected to our social media to hear words, that really, increasingly show us who we are, each one of us, and we know that we are all equal, no exception. and, that we must do good, so that we can dream about what we all want: peace" (tvbrasilgov 2020). in this part, bolsonaro calls for everyone to "be equal: without exception," returning to the idea that before god, everyone would be equal and that everyone should "do good" (tvbrasilgov 2020). then relates two important elements in christian social unity in brazil: "the practice of good" and the struggle for "peace" (tvbrasilgov 2020). after this initial speech, he gives the room to the religious, and, at the end of the video, he resumes the word (tvbrasilgov 2020). with this speech, he says that he had already gone to the saturday night video scene: about the stab he suffered at the end of 2018. compare the attack to jesus christ's final trajectory: "i confess that today was a special day for me, since today there is talk of resurrection. i didn't die, but i was there on the edge of death" (tvbrasilgov 2020). in this video, in a more acute way, he points out the relationship of his trajectory with the person of jesus christ, affirming that it was a miracle to have survived and resurrected to win the elections (tvbrasilgov 2020). for this reason, he puts himself in the place of the country's "savior." he justifies this by stating that he "did not have a profile of reaching the presidency." bolsonaro hints that this was part of the miracle performed by the divine in his life. as he says: he left "(almost) death" (tvbrasilgov 2020) for the mission of the presidency of the republic. by this practice, he calls himself as "god's chosen" (tvbrasilgov 2020). for this reason, he has the task of taking care of the country against the chaos the opositors are trying to build by the coronavirus account. hence, it is praised that "the responsibility is very great, the carrying cross very heavy, with millions of people on my side, who have a green and yellow heart, who believe in god, i believe that we can overcome obstacles" (tvbrasilgov 2020). he extols patriotism by linking himself to the metaphor of jesus' crucifixion, with the expression "the cross is very heavy." again, he defends his thesis of identification with christ to be recognized as the nation's messiah. by the video's ending, he says again about the quarantine issue: "since the beginning, forty days ago we have had two very serious problems, the virus and unemployment. forty days the commencing of the virus' end, but the issue of unemployment is hitting hard, but we must hit hard on these two things. obviously we always fight, we believe in god above all, we will overcome obstacles" (bolsonaro 2020b) . and, again in the reasoning of the "virus or unemployment", follows what butler (2020) emphasizes as "an eugenic logic", justified by the government's ultraliberal economist emphasis. hence, that so-called political "messiah" admits the "death of the poor, the weakest" (butler 2020), placing the inevitability measureness in the face of the coronavirus pandemic disaster in brazil (tvbrasilgov 2020). what it indicates is something serious, when in the middle of the event with christian leaders, it takes on a tone of christian appeal, in order to be able to mobilize even more its message as a political christ of the nation for the religious sector. as pointed out during the covid-19 pandemic period, bolsonarism (almeida 2019) broadcasts its discourse with messianic tones of political salvation in the country. it promotes such an operation "building scenes and hermeneutics" (rancière 2012 ) that make explicit an authoritarian political theology (schmitt 1988), reverberating contempt for the older population, with chronic health problems in the face of the possibility of death. it does this in order to recover its social base, building a false dichotomy between the social chaos of the quarantine and the unemployment that can plague the country. as listed in the article, during the temporality of easter 2020, he wove a strategy of investing heavily in the christian and messiah appeal, giving varied and "public evidence of being a good christian" (py 2019) : he showed to have knowledge of history of christianity, the bible, and mainly key biblical fragments. and with that, he painted himself as a christian messiah to mobilize his conservative religious base. therefore, bolsonarism underlines a "biblical war" (py 2020), fought within the brazilian state, spreading biblical verses as an easy and "holy" way of communicating with christian fundamentalism. this "biblical war" driven by bolsonaro is a bridge of direct dialog with fundamentalism, at the same time that it surrounds it with a despotic political theology, carried by an authoritarian messianism, which sacrifices the popular strata. bolsonaro's political intention is to promote, with biblical discourse, an attempt to relativize quarantine, putting at risk parts of the population "that can be discarded, killed" (mbembe 2014). when he draws his messianic authority by relativizing quarantine (or saying that the virus has passed), he comes close to the ideas of the typical social eugenics so operated in the past by fascist governments. for this reason, bolsonarism must account for the thousands of deaths that are already accounted for in the brazilian territory by victims of covid-19. bolsonaro presidente: conservadorismo, evangelicalismo e a crise brasileira pronunciamento do presidente da republica, jair bolsonaro (08/04/2020). youtube, 8 de abril de 2020 capitalism has its limits descolonização epistemológica da teologia. concilium os intelectuais e a organização da cultura. civilização brasileira, rio de janeiro igreja batista getsêmani (2020) clamor e jejum pelo brasil -05 abril -convocação do presidente celeste porvir: a inserção do protestantismo no brasil. são paulo, edusp py f (2019) a cristologia cristofascista de jair bolsonaro. carta maior py f (2020) pandemia cristofascista atuação de religiosos luteranos nos movimentos sociais rurais no brasil evangélicos e governo bolsonaro: aliança nos tempos de covid-19 la méthode de l'égalité. bayard, montrouge rancière j (2014) ódio a democracia minneapolis tvbrasilgov (2020) celebração de pascoa no palácio da alvorada missão como com-paixão. por uma teologia da missão em perspectiva latino-americana publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. key: cord-329536-3xsncmyi authors: passos, lígia; prazeres, filipe; teixeira, andreia; martins, carlos title: impact on mental health due to covid-19 pandemic: cross-sectional study in portugal and brazil date: 2020-09-17 journal: int j environ res public health doi: 10.3390/ijerph17186794 sha: doc_id: 329536 cord_uid: 3xsncmyi mental health effects secondary to the covid-19 pandemic were till recently considered less important or were neglected. portugal and brazil are facing the pandemic in quite different ways. this study aimed to describe the mental health status of the general adult population in portugal and brazil during the covid-19 pandemic and analyze the differences between the two countries. a cross-sectional quantitative study was based on an online questionnaire. socio-demographic data were collected in addition to four validated scales: cage (acronym cut-annoyed-guilty-eye) questionnaire, satisfaction with life scale, generalized anxiety disorder-7 and patient health questionnaire-2. for each outcome, a multiple linear regression was performed. five hundred and fifty people answered the questionnaire (435 women). the median age was 38 (q1, q3: 30, 47) years, 52.5% resided in brazil and 47.5% in portugal. the prevalence of anxiety was 71.3% (mild anxiety was present in 43.1%), the prevalence of depression was 24.7% and 23.8% of the sample had both depression and anxiety. isolation was a significant factor for depression but not for anxiety. well-being was below average. mental illness was considerably higher than pre-covid-19 levels. portugal and brazil will have to be prepared for future consequences of poor mental health and contribute immediate psychological support to their adult populations. during the current global health crisis, caused by the declaration of the coronavirus disease 2019 (covid-19) outbreak as a pandemic on 11 march 2020 by the world health organization (who) [1] , countries' main efforts are concentrated on implementing measures to prevent, control and treat the illness caused by the severe acute respiratory syndrome coronavirus 2 (sars-cov-2), along with research to develop a vaccine. the first positive case was registered in brazil on 26 february 2020 [2] and in portugal on 2 march 2020 [3] . in brazil, the first death from covid-19 occurred on march 12 [4] and 4 days later the same happened in portugal [5] . portugal and brazil are facing the pandemic in quite different ways. the government of portugal acted quickly with health precautionary measures, contingency plans and political union. on 18 march 2020, a national state of emergency was declared, suspending some citizens' rights so that public health protection measures could be implemented. some of the measures adopted throughout the countries of the impact on the emotional well-being of the decrease in interpersonal contact due to covid-19. this is a cross-sectional quantitative study based on an online questionnaire conducted from 27 may to 8 july 2020, among adults from the general population living in portugal or brazil. for inclusion in the study, participants should be residents in portugal or brazil, be over 18 years old, give their informed consent and agree to participate in the study. the questionnaire was built in the google forms platform and the questionnaire web link was sent by e-mail to the researchers' contact network, and through community groups in social networks, thus generating a snowball sample, where invited respondents shared the online questionnaire with their contacts. socio-demographic and other factors: variables assessed included age, gender, country of residence (portugal or brazil), marital status, educational level, employment status, social isolation self-label, duration of social isolation, living arrangements during social isolation, diagnosis of covid-19, alcohol consumption and alcohol addiction measured by the presence of two or more positive answers to the four-item cage (acronym cut-annoyed-guilty-eye) questionnaire [33, 34] translated and validated for the portuguese language [35] . satisfaction with life scale (swls): a global cognitive measure of satisfaction with one's life [36, 37] . it consists of five items rated on a five-point likert scale, ranging from 1: "strongly disagree" to 5: "strongly agree". this scale was translated and validated for the portuguese language [38] . a total score is obtained by the sum of the five items (range from 5 to 25 points). cronbach's alpha for this scale was 0.87 as reported by diener et al. (1985) [37] and 0.88 for the current sample. generalized anxiety disorder-7 (gad-7): a brief self-report scale to identify probable cases of generalized anxiety disorder and assess its severity in both the primary care setting and the general population [39] [40] [41] . the seven items of this instrument are scored on a four-point likert scale where 0: "not at all"; 1: "several days"; 2: "more than half the days"; and 3: "nearly every day". a total score is obtained by the sum of the seven items (range from 0 to 21 points). the cut-off points for classifying the severity of anxiety are: 0-4 = none/normal, 5-9 = mild, 10-14 = moderate and 15-21 = severe. gad-7 was validated for the portuguese language by sousa et al. (2015) [42] . in the present study, gad-7 was found to have excellent internal consistency (cronbach's alpha of 0.90). for the purpose of the current study, a total score of five points or above was used to indicate the possible presence of anxiety [42] . patient health questionnaire-2 (phq-2): a two-item depression screener. it includes the first two items of the phq-9 [43, 44] and evaluates the frequency of depressed mood and anhedonia. some authors consider phq-2 more explanatory than using all the phq-9 questions [45] . the two items of this instrument are scored on a four-point likert scale where 0: "not at all"; 1: "several days"; 2: "more than half the days"; and 3: "nearly every day". the sum score ranges from 0 to 6 points. a total score of 3 or above indicates that major depressive disorder is likely [46, 47] . in the present study, phq-2 was found to have good internal consistency (cronbach's alpha of 0.83). data analysis was performed using spss 26.0 version statistical software (ibm, armonk, ny, usa) and jamovi (version 1.2) (computer software, sydney, australia). categorical variables were described using absolute and relative frequencies, n(%) or (n; %). the prevalences are presented with the respective 95% confidence intervals. continuous variables not normally distributed were described by the median and the interquartile interval, mdn (q 1 , q 3 ). the normality of continuous variables was assessed by observation of q-q plots. the comparison of continuous variables between portugal and brazil was made by the mann-whitney test since the variables were not normally distributed. the comparison of categorical variables was made by the chi-squared test. for each outcome-satisfaction with life (swls), anxiety (gad-7) and depression (phq-2)-a separated multiple linear regression was performed. to decide which independent variables to include in each multiple regression, simple linear regressions were performed with each variable in the dataset, including socio-demographics, variables related to covid-19 and emotional variables, were obtained from questionnaires: satisfaction with life (slws), anxiety (gad-7) and depression (phq-2). all variables that correlated with the outcomes at p ≤ 0.20 in a simple regression were included in the multiple linear regressions [48] . only the significant variables were maintained in the final multiple models. the results of linear regressions were presented by the coefficient values (β) and the respective p-value. to evaluate the model, the determination coefficient (r 2 ) was presented. assumptions of the linear regression models were verified as follows: (1) visual analysis of histograms to assess the normality of residuals and (2) plotting residuals versus the fitted predictive values for checking homoscedasticity. values of p ≤ 0.05 were considered significant. the sum of the portuguese and brazilian populations over 18 years of age are approximately 164,058,140 [49, 50] . the minimum sample size (n = 385) was calculated for proportions and considering the most conservative scenario (a proportion of 50%), a population of 164,058,140 individuals, a level of confidence of 95% and an error margin of 5%. the present study followed the declaration of helsinki ethical standards and was approved by the ethics committee of the university of beira interior (ce-ubi-pj-2020-041). electronic consent was obtained from all participants. responses were anonymous. the questionnaire was answered by 550 participants, 289 (52.5%) residing in brazil and 261 (47.5%) in portugal. this sample size corresponds to a margin of error of 4.18% (in the same conditions of the sample size calculator). all participants fully completed swls, gad-7 and phq-2 instruments. no participants were excluded from the analysis. the characteristics of the participants are summarized in table 1 . most of them were female (435; 79.5%). the median age was 38 (q1, q3: 30, 47) years. regarding marital status, 290 (52.8%) were married or cohabiting. the level of education was high, with 51.3% (n = 282) being postgraduates, masters or phds and 61.6% (n = 335) declared being employed. notice that 88.2% of participants (n = 485) were in social isolation, with a median duration of 70 (q1, q3: 60, 90) days, and of these 485 participants, 81.4% (n = 395) had experienced more than 51 days in social isolation. most participants (383; 69.6%) lived with their families during this period. only 12.2% of participants (n = 67) were tested for covid-19 and only 1.3% (n = 7) tested positive. more than half (310; 56.4%) reported consuming alcoholic beverages. alcohol addiction (two or more points on cage) was present in 10.3% (n = 31) of the respondents, without a statistical difference between the residents of the two countries (chi-squared test; p = 0.995). a chi-squared test of independence was performed to examine the relation between the country of residence and isolation. residents in brazil were more likely than residents in portugal to isolate (p = 0.003); and the length of the isolation period was more likely to be longer than 51 days in brazil (p < 0.001). respondents scored slightly below average in life satisfaction (swls), with a median score of 18 (q1, q3: 14, 21) points and there were no significant differences between residents of portugal and brazil (p = 0.292; table 2 ). considering gad-7, the median score was 6 (q1, q3: 4, 11) points, also without significant differences between residents of portugal and brazil (p = 0.113; table 2 ). the prevalence rate of anxiety was 71.3% (95% ci, 67.5-75.1) (mild anxiety was present in 43.1% (95% ci, 39.0-47.2), moderate anxiety in 17.6% (95% ci, 14.5-21.1) and severe anxiety in 10.5% (95% ci, 8.0-13.1) of the sample). the median phq-2 score was 2 (q1, q3: 0, 2) points and residents of brazil had a slight but significantly higher median score than portuguese ones (2 vs. 1, p = 0.040; table 2 ). the prevalence rate of depression was 24.7% (95% ci, 21.1-28.3) and 23.8% (95% ci, 20.3-27.4) had both depression and anxiety. no differences were found in the prevalence of having both anxiety and depression between the portuguese and brazilian subgroups (p = 0.059 and p = 0.273, respectively; table 2 ). gender, educational level, professional status, co-living status and depression (phq-2 score) were found to be significant factors for life satisfaction (swls) in multiple linear regression (r 2 = 0.211; table 3 ). women's life satisfaction scores were higher by an average of 1.08 in comparison to men (p = 0.027). higher levels of education were significantly associated with increased levels of life satisfaction scores (β = 1.81, p = 0.006). students' life satisfaction scores were higher by an average of 1.56 in comparison to employees (p = 0.002). those who lived with family members or with a partner in the period of social isolation were significantly associated with increased levels of life satisfaction (β = 1.59, p = 0.023 and β = 2.53, p = 0.001, respectively). higher levels of depression (phq-2) were significantly associated with a reduction of life satisfaction levels (β = −1.26, p < 0.001). gender and depression (phq-2 score) were found to be significant factors for anxiety (gad-7) in multiple linear regression (r 2 = 0.462; table 4 ). women's anxiety levels were higher by an average of 0.88 in comparison to men (p = 0.020). higher levels of depression (phq-2) were significantly associated with an increase in anxiety levels (β = 2.03, p < 0.001). table 4 . regression coefficients for generalized anxiety disorder-7 (gad-7) as an outcome with socio-demographic and emotional variables as predictors, from univariate multiple linear regressions. social isolation, life satisfaction (swls) and anxiety (gad-7) were found to be significant factors for depression (phq-2) in multiple linear regression (r 2 = 0.519; table 5 ). being in social isolation was significantly associated with an increase in depression levels (β = 0.33, p = 0.026). higher levels of life satisfaction (swls) were significantly associated with a reduction of depression levels (β = −0.07, p < 0.001). higher levels of anxiety (gad-7) were significantly associated with an increase in depression levels (β = 0.20, p < 0.001). all levels of anxiety had a significant association with the phq-2 scale, in comparison with the group without/normal anxiety levels. those with severe anxiety had a depression level that was on average higher by 3.14 (p < 0.001). to the extent of the authors' knowledge, the present study is the first to analyze the mental health status of the general adult population in portugal and brazil during the covid-19 pandemic. it has been previously expressed that mental health conditions are going to be the great pandemic of this century [51] and, to some extent, the results of the current study corroborate this statement. in the present study, the prevalence of anxiety was 71.3% (mild anxiety was present in 43.1%), the prevalence of depression was 24.7% and 23.8% of the sample had both depression and anxiety. the observed frequency of mental illness was considerably higher than pre-covid-19 levels, as expected from the results of previous studies that suggested a connection between a public health crisis and mental health conditions [52, 53] . even before the covid-19 outbreak, brazil had the highest prevalence of anxiety among all countries in the world, with 9.3% of the population having some type of anxiety disorder. at the same time, the prevalence of anxiety in portugal was 4.9%. regarding depressive disorders, the prevalence was similar in both countries (5.7% vs. 5.8% for portugal and brazil, respectively) [54] . even though the studies were done during the initial stage of the covid-19 outbreak [16] and used different scales or populations so no direct comparison between studies is possible, the present study showed a similarly high prevalence of mental health conditions (e.g., the prevalence rate of depression was 50.7% and that of generalized anxiety was 44.7% in a multicenter study involving around one and a half thousand chinese medical workers [55] ). it can thus be suggested that the covid-19 pandemic has significantly affected the mental health of the general adult population in portugal and brazil, with an increased risk of future challenges of impairment, alcohol or drug coping, negative religious coping, hopelessness and suicidal ideation, as was the case in other samples with high levels of anxiety related to covid-19 [56] . female gender was associated with higher levels of psychological distress in the time of covid-19 [16] . in the present study, women were associated with higher rates of anxiety but not depression. this finding is contrary to previous studies which have suggested that women are at higher risk of anxiety and depression [57, 58] . this inconsistency may be due to the effect of the current public health crisis on the use of coping strategies, like positive reframing [59] . although females showed higher anxiety in comparison to males, this did not affect their self-rated life satisfaction. this could be an important issue for future research. in portugal, the social confinement lasted about 51 days for many people [21] (and much more in brazil, although with state dissimilarities), despite that, the individuals that were isolated had higher depression levels. this result suggests that social isolation may be a risk factor for depression, in agreement with the results obtained by previously published research [60, 61] , and this may be even more evident when a quarantine is imposed [20] or if loneliness is present [62] . one interesting finding of this study was that during the ongoing covid-19 pandemic, anxiety and depressive disorders continue to be particularly comorbid [63] , with higher levels of depression being significantly associated with increasing levels of anxiety and vice versa. prior studies have noted that almost half of depressive individuals (45.7%) have had an anxiety disorder during their life [64] and that 42% of individuals with anxiety have had at least one episode of depression in their life [65] . an implication of the current study's results is the possibility that individuals experiencing the covid-19 pandemic are at higher risk of developing more severe symptoms and poor treatment response for depression/anxiety [66] . regarding the impact of the covid-19 pandemic on well-being, respondents scored slightly below average on the life satisfaction scale (swls), without significant differences between residents of portugal and brazil; these scale results may be due to the presence of a meaningful problem in only one area of their lives, or more likely, in the current pandemic crisis, to the presence of problems in several areas of the respondents' lives [67] , from multiple potential stressors, such as respondents' worries for their finances, health or those close to them, social isolation and loneliness, loss of pre-covid routines and contact with former sources of positive reinforcement [68] , which in turn may increase the risk of depression. some of these areas were confirmed by the significant factors for life satisfaction found in multiple linear regression: professional status, educational level, co-living status and depression. in the present sample, a considerable effect on the well-being of working individuals (that students would not experience) may be due to the presence of feelings of anxiousness regarding future work and finances and this may be even more prominent in individuals with lower educational levels whose jobs are not suitable for teleworking (or remote working) during social distancing measures [69] . an implication of this is the possibility that workers with low educational levels may benefit from being well informed about their sick pay and benefits rights during the current pandemic. some limitations must be considered when interpreting the results of the present study. one limitation concerns convenience sampling and, although it was carried out in two countries, it still does not allow for the generalization of results since respondents shared similar demographic characteristics. the lack of a diverse sample limits the ability to explore how some demographic characteristics (e.g., socioeconomic status) may affect mental health during the pandemic. portugal and brazil faced the pandemic in different ways (e.g., social distancing measures), and distinct societal and economic characteristics between the two can still have an impact on the mental health of each population and may increase poverty and inequalities between the two countries. some risk factors of poor mental health (or its protective factors) were not collected and therefore their role in determining the results of the present study cannot be calculated. further work is needed to evaluate the social, environmental and economic determinants of mental health in the covid-19 pandemic. the role of uncertainty stress on the development of mental ill-health should also be studied. another limitation is the fact that no information regarding the previous mental health of the participants was collected. thus, it is not possible to analyze the extent to which the covid-19 pandemic contributed to an expected worsening of depressive and anxiety symptoms. future longitudinal studies could contribute to a better understanding of the late effects of social isolation on the mental health of adults. evidence suggests that the presence of mental illness was considerably higher than pre-covid-19 levels, both in portugal and brazil. the prevalence of anxiety was 71.3% (mild anxiety was present in 43.1%), the prevalence of depression was 24.7% and 23.8% of the sample had both depression and anxiety. consequently, well-being was below average. portugal and brazil will have to be prepared for future consequences of poor mental health and contribute immediate psychological support to their adult population. the development and improvement of mental health public policies must be an essential part of governments' response to the covid-19 pandemic, with a commitment to support and care for affected individuals. the first step should be to campaign to raise public awareness about mental illnesses so not only those with issues seek early help but also those who are at increased risk (e.g., females and those in social isolation). mental health services must be expanded and widely funded, as part of the universal health coverage, and health professionals should be knowledgeable regarding the risk factors and protective factors of mental disorders and be able to provide in-person or virtual counseling or therapy. to improve well-being during a crisis like the covid-19 pandemic, there is the need to maintain social connections, decrease isolation and care for the mental health of individuals by the use of, for example, phone calls or video chats with friends and loved ones. governments should also protect employees from being fired for being in quarantine or social isolation. who director-general's opening remarks at the media briefing on covid-19-11 brasil confirma primeiro caso da doença ministra confirma primeiro caso positivo de coronavírus em portugal morte por coronavírus no brasil aconteceu em 12 de março, diz ministério da saúde registada primeira morte por novo coronavírus em portugal rapid assessment of the impact of lockdown on the covid-19 epidemic in portugal antónio costa anuncia fim do estado de emergência e declara estado de calamidade major brazilian cities set lockdowns as virus spreads forced social isolation and mental health: a study on 1006 italians under covid-19 lockdown mental healthcare for psychiatric inpatients during the covid-19 epidemic timely mental health care for the 2019 novel coronavirus outbreak is urgently needed the outbreak of covid-19 coronavirus and its impact on global mental health the forgotten plague: psychiatric manifestations of ebola, zika, and emerging infectious diseases multidisciplinary research priorities for the covid-19 pandemic: a call for action for mental health science mental health outcomes of the covid-19 pandemic survey results: understanding people's concerns about the mental health impacts of the covid-19 pandemic social isolation among older individuals: the relationship to mortality and morbidity the impact of the covid-19 pandemic on mental health the psychological impact of quarantine and how to reduce it: rapid review of the evidence quais são os riscos para a saúde mental? rev. port. psiquiatr. e saúde ment. 2020 mental health outcomes of quarantine and isolation for infection prevention: a systematic umbrella review of the global evidence understanding, compliance and psychological impact of the sars quarantine experience alcohol abuse/dependence symptoms among hospital employees exposed to a sars outbreak family violence and covid-19: increased vulnerability and reduced options for support related health factors of psychological distress during the covid-19 pandemic in spain depression and anxiety in hong kong during covid-19 effects of covid-19 lockdown on mental health and sleep disturbances in italy covid-19 pandemic: age-related differences in measures of stress, anxiety and depression in canada census bureau-assessed prevalence of anxiety and depressive symptoms in 2019 and during the 2020 covid-19 pandemic europa endurece medidas face a ameaça de segunda vaga da covid-19 sapo. das máscaras obrigatórias aos casamentos com 10 pessoas, países voltam a apertar regras contra a covid-19 detecting alcoholism. the cage questionnaire the cage questionnaire: validation of a new alcoholism screening instrument validation of the "cage" alcoholism screening test in a brazilian psychiatric inpatient hospital setting. braz review of the satisfaction with life scale the satisfaction with life scale ulterior validação de uma escala de satisfação com a vida (swls) anxiety disorders in primary care: prevalence, impairment, comorbidity, and detection validation and standardization of the generalized anxiety disorder screener (gad-7) in the general population a brief measure for assessing generalized anxiety disorder: the gad-7 reliability and validity of the portuguese version of the generalized anxiety disorder (gad-7) scale. health qual the phq-9: a new depression diagnostic and severity measure the phq-9: validity of a brief depression severity measure screening for depression: rasch analysis of the dimensional structure of the phq-9 and the hads-d study of the discriminative validity of the phq-9 and phq-2 in a sample of brazilian women in the context of primary health care the patient health questionnaire-2: validity of a two-item depression screener classical and modern regression with applications total e por grandes grupos etários instituto brasileiro de geografia e estatística (ibge). população, por grupos de idade a saúde mental vai ser a grande pandemia deste século long-term psychiatric morbidities among sars survivors ebola outbreak and mental health: current status and recommended response depression and other common mental disorders: global health estimates; world health organization online mental health services in china during the covid-19 outbreak coronavirus anxiety scale: a brief mental health screener for covid-19 related anxiety gender differences in unipolar depression: an update of epidemiological findings and possible explanations prevalence of depression in the community from 30 countries between 1994 and 2014/692/699/476/1414/692/499 article sex differences in the use of coping strategies: predictors of anxiety and depressive symptoms an overview of systematic reviews on the public health consequences of social isolation and loneliness perceived social isolation, evolutionary fitness and health outcomes: a lifespan approach social isolation, loneliness and their relationships with depressive symptoms: a population-based study the critical relationship between anxiety and depression anxious and non-anxious major depressive disorder in the world health organization world mental health surveys psychiatric comorbidity in patients with generalized anxiety disorder clinical characteristics and treatment outcomes of patients with major depressive disorder and comorbid anxiety disorders -results from a european multicenter study understanding scores on the satisfaction with life scale covid-19: psychological flexibility, coping, mental health, and wellbeing in the uk during the pandemic ability to work from home: evidence from two surveys and implications for the labor market in the covid-19 pandemic this article is an open access article distributed under the terms and conditions of the creative commons attribution (cc by) license key: cord-295554-0pzjyrdf authors: lima, francisco esmaile de sales; campos, fabrício souza; kunert filho, hiran castagnino; batista, helena beatriz de carvalho ruthner; carnielli júnior, pedro; cibulski, samuel paulo; spilki, fernando rosado; roehe, paulo michel; franco, ana cláudia title: detection of alphacoronavirus in velvety free-tailed bats (molossus molossus) and brazilian free-tailed bats (tadarida brasiliensis) from urban area of southern brazil date: 2013-03-16 journal: virus genes doi: 10.1007/s11262-013-0899-x sha: doc_id: 295554 cord_uid: 0pzjyrdf a survey was carried out in search for bat coronaviruses in an urban maternity roost of about 500 specimens of two species of insectivorous bats, molossus molossus and tadarida brasiliensis, in southern brazil. twenty-nine out of 150 pooled fecal samples tested positive by reverse transcription-pcr contained fragments of the rna-dependent rna polymerase gene of coronavirus-related viruses. the sequences clustered along with bat alphacoronaviruses, forming a subcluster within this group. our findings point to the need for risk assessment and continued surveillance of coronavirus infections of bats in brazil. electronic supplementary material: the online version of this article (doi:10.1007/s11262-013-0899-x) contains supplementary material, which is available to authorized users. bats (order chiroptera, suborders megachiroptera and microchiroptera) are one of the most diverse and widely distributed groups of mammals, representing *20 % of all known mammalian species [1] . about a 100 different viruses have been identified in bats of different species in asia, europe, north america and africa. therefore, such species may be natural reservoirs for a large variety of potentially zoonotic rna viruses, such as lyssaviruses, paramyxoviruses, ebola and marburg viruses as well as the recently emerged severe acute respiratory syndrome coronavirus (sars-cov) [2] [3] [4] [5] [6] . a variety of other coronaviruses have been detected in many bat species from asia, including specimens of the genus rhinolophus, which were found to be infected with sars-like cov. phylogenetic analyses of such viruses revealed that those form a large clade within betacoronavirus genus, along with sars coronaviruses from palm civets and the sars coronaviruses recovered from humans during the 2003 outbreak [7, 8] . these data suggested that the agent responsible for the 2002-2003 pandemic might have originated from bats. in addition, in 2012, a new human coronavirus (hcov-emc), which has been associated to clinical disease that resembles sars, emerged in the middle east. this new virus appears to have originated from bats, raising the possibility that hcov-emc jumped species directly from bats to humans [9] . in brazil, most studies looking for associations between bats and viruses have focused on the role for those species as reservoirs for rabies virus [10] . however, to date, more than 160 bat species have been detected in brazil, comprising members of the families phyllostomidae, vespertilionidae, and molossidae. it is estimated that at least 40 bat species live in the state of rio grande do sul, southern brazil, where the predominantly sub-tropical climate seems to favor the settlement of such species [11] . in view of the potential role that bats may play in the transmission of new viral infections to humans and other species, this study was set up in search for coronavirus genomes in bats from the urban area of porto alegre (30°01 0 59 00 s; 51°13 0 48 00 w), a town with about 1.5 million inhabitants and capital of the state of rio grande do sul, brazil. with that purpose, coronavirus rna was searched in feces of two species of synanthropic insectivorous bats collected in a maternity roost within the urban area of the city. a maternity roost of bats known to have direct contact with people and domestic animals was identified in the summer of 2012 in the attic of a residence in the central area of porto alegre, southern brazil. the colony was estimated to harbor about 500 bat specimens of insectivorous bats of two species, velvety free-tailed bats (molossus molossus) and brazilian free-tailed bats (tadarida brasiliensis). speciation was confirmed by amplification and sequencing of the mitochondrial cytochrome b (cytb) gene as described [12] . one hundred and fifty fecal samples were collected from the attic floor as follows: a plastic film was spread on the ground of the attic compartment and fresh droppings were collected with clean disposable forks in the following night. each sample consisted of five fecal droppings, which were immediately sent to the laboratory and stored at -80°c. the samples were then submitted to total rna extraction with trizol (invitrogen tm ). cov rna screening was performed by reverse transcription-polymerase chain reaction (rt-pcr) in a total volume of 25 ll reaction using conserved primers for the rna-dependent rna polymerase gene (forward: 5 0 -ggttgggactatc ctaagtgtga-3 0 and reverse: 5 0 -ccatcatcagatag aatcatcata-3 0 ). this pair of primers is expected to give rise to amplicons of 440 bp [7] . the cycling conditions were: 5 min at 94°c followed by 35 cycles of 1 min at 94°c, 1 min at 49°c and 1 min at 72°c, followed by a final extension time of 5 min at 72°c. bovine coronavirus (bcov) rna was used as a positive control to optimize the assay. standard precautions were taken to avoid pcr contamination; blank controls without template were included in every set of five rt-pcr assays. five microliters of the pcr products were electrophoresed in 1.5 % agarose gels and the products visualized on uv light after staining with ethidium bromide. the amplicons obtained were cloned into pcr ò 2.1-topo ò cloning kit (invitrogen) before being submitted to nucleic acid sequencing. sequencing was performed with the big dye terminator cycle sequencing ready reaction (applied biosystems, uk) in an abi-prism 3100 genetic analyzer (abi, foster city, ca), following the manufacturer's protocol. sequence analyses were performed with the blast software [13] . nucleotide sequences were aligned and compared to human and animal cov sequences available at genbank database with the program clustalx 2.0 [14] . alignments were optimized with the bioedit sequence alignment editor program version 7.0.9 [15] . the protocol to generate the phylogenetic trees was selected with the program modeltest 3.7 [16] . phylogenetic analysis was carried out using mega 5.0; pairwise genetic distances were calculated by the tamura 3-parameter model and phylogenetic trees were constructed using the neighbourjoining method. bootstrap values were determined by 1,000 replicates to assess the confidence level of each branch pattern. pcr amplicons with the expected size of the targeted region were obtained from 29 out of the 150 (19.33 %) pools of bat fecal samples. the nucleotide sequences of sixteen randomly selected amplicons were determined and submitted to genbank (accession numbers kc 110770 to kc 110785). genetic analyses provided evidence that the viruses circulating in these two species of insectivorous bats belong to the genus alphacoronavirus. when compared with each other, all the obtained sequences showed a high nucleotide and amino acid identity (90.6 to 100 % and 98 to 100 %, respectively) (supplemental material). the rdrp sequences examined here were distantly related (\75 % nt identity) to other known alphacoronaviruses. the closest bat coronaviruses rdrp sequences found in genbank were the asian (btcov/a633/2005) and north american (rm-btcov 6 and rm-batcov 11) bat coronaviruses (fig. 1) . the percentage of nucleotide similarity between the sequences described here and those of asian and north american coronaviruses ranged from 72.4 to 76 %, whereas at the amino acid level, the similarity ranged from 74 to 81 % (data not shown). during the last two decades, several studies have shown that various important human and animal pathogens are of bat origin; these species have become targets for several surveillance studies aiming the detection of other potentially pathogenic viruses for humans and other animals. the association of these pathogens and possible disease outbreaks caused by direct or indirect contact of humans with bats stimulated the development of research activities on bat-borne viruses. in addition, the advances of molecular techniques offer opportunities for the discovery of novel dna and rna bat viruses without the need for virus isolation and bat pooled fecal samples being used as source for viruses, preventing animal manipulations [17, 18] . in our study, we detected rdrp sequences of bat cov at a frequency of 19.33 % in the examined samples; such frequency is comparable to previous results obtained in similar studies from different bat species in other countries (ranging figure) . the tree was generated based on the neighbor joining method in the mega program. the nucleotide sequence of the equivalent genome fragment of sars-cov was included as outgroup (fig. 1) . these results show that similar coronaviruses are found in different bat species that are distributed in geographically distant regions, suggesting a low degree of host restriction for coronavirus in those bat populations. in contrast to the enormous diversity of cov genomes found in old world bats [12, 25] , in this study and in several others concerning the cov detection in new world bats, only alphacoronaviruses were detected [2, 3, 17, 18] . based on these results, it has been hypothesized that covs found in new world bats are less diverse than those detected among old world bats [26] . in this initial study, samples were restricted in location and variety of bat species, and we found only alphacoronaviruses. such findings do not reflect data on incidence or prevalence of such infections in bat populations. however, one cannot exclude the possibility that a greater diversity may become apparent in brazilian bats as long as larger numbers of samples from a wider spectrum of species are examined. to our knowledge, this is the first report of cov detection in feces from presumably healthy insectivorous bats in brazil. however, it is very likely that other bat species might also be infected with similar viruses. additional studies with larger numbers of bats and bat species, as well as the continued vigilance on the occurrence of viral infections in bats over the years is required to follow the evolution of bat coronaviruses in its interactions with the different bat host species. in addition, the detection of covs in brazilian bat populations in close proximity to human inhabitants may represent a risk to human health. our findings point to the need to identify the prevalence of covs in brazilian bats, to perform risk assessment studies and continued surveillance of coronavirus infections from both urban and rural environments. mammal species of the world: a taxonomic reference vector borne zoonotic dis proc. natl. acad. sci. usa bioedit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/nt acknowledgments we would like to thank the government agencies finep, cnpq, and capes by the financial support. p.m. roehe, a.c. franco, and f.r. spilki are cnpq research fellows. key: cord-127293-mujyq3kk authors: neto, osmar pinto; reis, jose clark; brizzi, ana carolina brisola; zambrano, gustavo jose; souza, joabe marcos de; pedroso, wellington amorim; pedreiro, rodrigo cunha de mello; brizzi, bruno de matos; abinader, ellysson oliveira; kennedy, deanna m.; zangaro, renato amaro title: mathematical model of covid-19 intervention scenarios for sao paulobrazil date: 2020-05-18 journal: nan doi: nan sha: doc_id: 127293 cord_uid: mujyq3kk an epidemiological compartmental model was used to simulate social distancing strategies to contain the covid-19 pandemic and prevent a second wave in sao paulo, brazil. optimization using genetic algorithm was used to determine the optimal solutions. our results suggest the best-case strategy for sao paulo is to maintain or increase the current magnitude of social distancing for at least 60 more days and increase the current levels of personal protection behaviors by a minimum of 10% (e.g., wearing facemasks, proper hand hygiene and avoid agglomeration). followed by a long-term oscillatory level of social distancing with a stepping-down approach every 80 days over a period of two years with continued protective behavior. the world health organization (who) officially declared covid-19 a pandemic in march of 2020 1 . two months later over 4.3 million people have tested positive for the virus resulting in more than 300,000 deaths worldwide 2 . most countries, including brazil, have implemented widespread social distancing (sd) restrictions in an effort to mitigate the spread of covid-19. it appears, from updated models, that these strategies have effectively reduced the number of cases and associated deaths compared to earlier predictions 3 . however, a new report indicated that sd measures in brazil have not been as effective at reducing the reproduction number (r0) as it has in other countries 4 . r0 represents the average number of secondary cases that result from the introduction of a single infectious case in a susceptible population 5 . the r0 for brazil is 2.81, while the r0 for china, for example, dropped to below 1 with sd measures in place 6 . a r0 = 2.81 indicates that brazil has not controlled the covid-19 pandemic. in fact, brazil is the new virus hot spot with the highest infection and death counts in latin america, with the state of são paulo considered one of the main hotspot 6 . são paulo is the most poulous state in brazil with over 46 million inhabitants. therefore, exploring alternative sd intervention strategies for brazil in general and são paulo specifically is of utmost importance. several factors may lead to differences in intervention strategies on covid-19 infection and death rates for são paulo, brazil compared to other states and countries. for example, research has indicated the older adults (60+) are at the greatest risk of experiencing complications from covid-19 7 . given that brazil has a large percentage of its population over the age of 60 years, especially in urban areas such as são paulo, the incidence of aggravated cases may be particularly high in comparison to places with younger population demographics 8 . it has also been debated whether environmental conditions influence the behavior of the covid-19 virus similar to the common cold and flu 9, 10 . yet, the majority of the research investigating the virus has been conducted in environments different/opposite than that of brazil and other areas in the southern hemisphere. in addition, brazil faces many economical and sociocultural challenges that may affect mitigation strategies differently than cities, states, and/ or countries that are the current focus of most prediction models 8 . therefore, the purpose of the current investigation is to model covid-19 sd intervention strategies on transmission dynamics in são paulo, brazil and to determine best-case scenarios. our model was able to accurately fit the corrected accumulated cases and deaths data for brazil and são paulo ( figure 1 ). on the day of the analysis (may 11, 2020), sd was estimated at 41% in brazil and 52% in são paulo and protection was 59% in brazil and 60% in são paulo. all optimized coefficients, as well as the latent period, infectious period, hospitalized period, icu period estimated from the model can be found in table 1 . considering the size of the country and that many regions are facing different stages of the pandemic, we concentrate further analyses in the state of são paulo. the results suggest that the optimal strategy was the stepping down strategy (figure 2a ,b) and optimal time window was 80 days (figure 2c ). the results suggest that by constraining sd and protection levels to realistic ranges (30 to 70% and 50 to 70% respectively), optimal solutions regarding strategies and time window to contain the first and second peak of the pandemic converge confirming the optimal strategy ( figure 2b ) and window ( figure 2c ) that can be observed in (figure 2a ) considering keeping the current sd and protection values and the optimal strategy and time window it would be possible to contain the first peak in the pandemic but not the second ( figure 1e) nevertheless, the results suggest that by keeping current sd, increasing protection by 10%, and using optimal strategy and time windows between 60-80 days, it is possible to contain the first peak and second peaks of the pandemic in são paulo (figure 1f ). after a 60 days period, a reduction in average sd across the reminder of the pandemic with 60-80-day windows steeping strategy would cause approximately a 30 thousand decrease in the number of critical cases over icu threshold in comparison to the 80-day window intermittent strategy and 100 thousand compared to the constant sd strategy. additionally, considering the stepping strategy, either a 60-80-day window would cause approximately 40 thousand decrease in the number of critical cases over icu threshold compared to a 40-day window. finally, considering increasing protection by 10% but having a drop in sd from 52% to 40%, optimal strategy and optimal time window suggest that critical cases over icu threshold would be approximately 30 thousand; at 80-day windows stepping strategy would cause approximately a 11 thousand decrease in the number of critical cases over icu threshold in comparison to the intermittent strategy and 100 thousand compared to the constant sd strategy ( figure 1g ). additionally, considering the stepping strategy, an 80-day window would cause approximately 50 thousand decrease in the number of critical cases over icu threshold compared to a 40-day window and 15 thousand compared to a 60-day window. we used a sueihcdr compartmental model to project thousands of scenarios for the transmission dynamics of covid-19 in são paulo, brazil through the next two years. we used advanced algorithms to model scenarios related to strategy type, sd magnitude, time window, and level of personal protection. the goal was to determine the best-case scenario to control the current peak of infections and avoid a second pandemic wave. currently, brazil has the highest rate of transmission in the world with an estimated r0 of 2.81 6 , indicating that it has yet to contain the first peak in infections and associated deaths due to the covid-19 pandemic. data from around the world (e.g., asia, europe, and north america) indicate that it is possible to mitigate the spread of covid-19 with widespread sd and ppm measures 3 . however, our analysis of location data 11, 12 indicate that the current level of sd is at only 42% for brazil and for 52% são paulo. in addition, the current protection values are 60% for the state and 69% for the country. not only does our model indicate that current sd and protection values are insufficient in controlling the pandemic, they will have dire consequences on the overall number of infections and associated deaths with an extremely large first peak. in addition, our model suggest that this will result in the need of public health resources, especially icu, exceeding what is currently available. with the current levels of sd and protection, our model predicts that the icu needed will surpass the available icu in sao paulo at the first drop of sd levels, unless protection increases ( figure 1 ). the scenario may be even worse because not all icu beds available are exclusively dedicated to covid-19 patients and because some cities may experience the health-care system failure before others. according to our model, it is possible for the state of são paulo to gain control over the first peak if levels of personal protection are significantly increases (at least 10%). alternatively, an immediately increase sd to values over 75% may solve the problem of the first peak as well. however, increasing sd to values in 75% may result in a second peak if the restrictions are lifted within 40days. sd at 75% represents a complete lock down 13 . thus, such a strategy should be used with caution. further, it should only be used in critical cities and not the state as a whole. our model suggest that if this high-level of sd is used, it is only necessary for a short time (until end of june 2020). note, however, that lower levels of sd will need to be in place for years to come to maintain control over the pandemic 14, 15 . widespread use of ppm (e.g., wearing facemasks, frequently washing hands, using hand sanitizer, maintaining physical distance between other people, and avoiding agglomerations) and high rates of testing have been emphasized to mitigating the spread of covid-19 in addition to sd [15] [16] [17] [18] [19] . the results of our model agree; our model indicates that an increase in personal protection to a level of 70% for são paulo in combination with sd is necessary to contain the concurrent peak in infections and associated deaths. eikenberry et al. (2020) estimated that the efficacy of using face masks ranges between 50 to 90%, depending upon mask material and fitting 20 . they assumed that at least 50% protection factor would be achievable for well-made and well-fitted mask usage by the entire population 20 . the fitting of our model predicts that current level of protection is about 60%. an increase in protection levels would need a massive effort by public health officials to enforce and/or educate people to use facemask and to maintain a 2 meters safe distance from other people. note, some brazilian cities have implemented strict sd guidelines and require some level of personal protection 19 . for example, belo horizonte, rio de janeiro, and salvador require facemasks in public 21 . são paulo recently announced they will require facemask as well. assuming that brazil can effectively reduce r0 below 1 with sd and personal protection, it is important to take steps to reduce the likelihood of a second peak. our models indicate that if sd and personal protection measures are stopped too soon or reduced too much after the containment of the first peak, a second peak in infections and associated deaths will occur. many experts agree that a secondary pandemic wave is likely if sd restrictions are lifted too quickly 22, 23 . therefore, determining when and how to relax restrictions has become the focus of epidemiological work around the world. it has been proposed that a responsible exit strategy should continue sd restrictions alongside widespread testing and contract tracing 24 . nevertheless, our models suggest it is possible for brazil, considering são paulo as a model state, to avoid a second peak. according to our results, the best-case exit strategy to prevent a second peak in são paulo was a stepping-down strategy over a two-year period. a stepping-down approach would involve a gradual stair-step down. for example, the steppingdown approach we modeled multiplied sd values of 40%, 30% and 20% by 1, then 1/2, then 1/4, then 1/8 and then back to 1 and the we repeated each stair-step down. a stepping-down strategy was also the best-case exit strategy modeled for the us 15 . a stepping-down approach may be beneficial because it allows for periods of transmission leading to heard immunity without overwhelming public health resources 14, 25 . alternatively, a one-time sd may result in a catastrophic second peak (figure 1 , yellow curve), if the virus reoccurred and not enough people have immunity 14, 25 . in addition, the stepping-down approach resulted in a 6.5% reduction in total time required to sd over the two-year period, potentially reducing the economic and social costs associated with sd. the results of the current investigation suggest that an 80-day window between each step was the most beneficial strategy. this result is also consistent with that for the us 15 . note, however, the current investigation modeled more time windows and more complex algorithms than the us model. in addition, the best-case stepping-down strategy with an 80-day windows was a magnitude of sd of at least 50%, in the highest windows, or approximately 24% average through the period of analysis. furthermore, the results suggest that higher protective measures could account for lower sd values, which may be associated with economic and/or psychological benefits. alternatively, higher sd values delay the onset of the second peak. delaying the onset of the peak may allow brazil to procure additional public resources and more time for the development of effective treatments or even a vaccine. the minimum protection rate for this scenario was 70% for são paulo. if protection rates are maintained at these levels the models suggest that a second peak would be avoided. this result provides additional support for the notion that personal protection is critical for maintaining control over the covid-19 pandemic [15] [16] [17] [18] [19] . the sueihcdr model we extended a generalized susceptible-exposed-infected-recovered (seir) compartmental model using factors specific to covid-19 26, 27 to investigate the covid-19 pandemic in the us. it is composed of eight compartments: susceptible, unsusceptible, exposed, infected, hospitalized, critical, dead, and recovered (sueihcdr) (figure 1 ). the furthermore, social distancing until present day was determined from mobility trends data from apple maps 11 and community mobility reports from google 12 . data were low-pass filter filtered at 0.09 hz (butterworth 4th order), and percentage changes from baseline were considered (apple's driving data was averaged with google's retail and recreation, grocery and pharmacy, parks, transit stations, and workplaces average percent change from baseline. from present day forward sd was manipulated in different windows of time to project possible future scenarios. we used the fourth order runge-kutta numerical method to solve our system of ordinary differential equation in matlab (mathworks inc.r14a). we used both accumulated case and deaths time series to fit the model, both corrected by a factor (table 1) . cases sub-test factor was calculated as the ratio between the death rate in iceland (country with the greatest percentage of test per inhabitant 28 ), corrected by age stratification (older adults (60+): 6.4%; senior older adults (80+): 13.4% 29 ). death sub-factor was determined comparing data from deaths in the last months to average deaths in the same period from past 5 years [30] [31] [32] . the resulting sub-factor was similar to that reported by other sources (https://www.ft.com/content/6bd88b7d-3386-4543-b2e9-0d5c6fac846c). fitting analysis was done with a custom build matlab global optimization algorithm using monte carlo iterations and multiple local minima searches ( figure 1 ). the algorithm was tested for the best solution considering all inputs varying within ranges obtained from the who 33 and several publications [34] [35] [36] (table 1) after model's coefficient were fitted an optimization workflow using esteco's mode frontier (esteco s.p.a; 2017r4-5.6.0.1) was implemented to find the optimal mitigation strategy out of the proposed here could be identified. future scenarios considered changes in sd and protection staring june 1 st , 2020. first, we run a doe (design of experiment) scheme of around 1000 sobol individuals and 1000 latin hypercube individuals created by varying maximum sd values per window within 0-75% and protection percentage between 20-95%. then data was constrained considering more realistic ranges of sd and protection (30 to 70% and 50 to 70%, respectively) (complete optimization analysis can be found in the supplementary file). we propose 3 strategies of mitigation ( figure 2 ): 1) a stepping-down strategy (starting at a specific sd, it is divided by half for the next 3 time windows, on the fourth time window sd is back to its initial value, and the process is repeated); 2) a standard intermittent sd strategy (a specific sd value alternates with periods of no sd); and 3) a constant sd strategy (sd is kept constant at as specific value); with each strategy considering three different times windows: 40, 60 or 80 days ( figure 3) . furthermore, strategies were compared using similar average sd across time; note however, that for because of its design when intermittent and stepping down strategies have the same maximum sd, and when adopting half of this values for the constant sd strategy, average sd values across time tends to be 6.25% smaller for the stepping-down strategy compared to the other two. a moga -multi objective genetic algorithm was used to drive the optimization, due to the discrete nature of the variables strategy and window. we minimize the number of critical cases over icu threshold (icu_e) for the duration of the analysis, the number of critical cases over icu threshold in the first peak of the pandemic (icue_1), the number of critical cases over icu threshold in the second peak of the pandemic (icue_2) and sd. paulo (c,d) with a 95% confidence interval and representative results for intensity care units bed occupancy per day (icu_pd; i.e. critical cases). e) shows 8 different cases with protection kept at current state level of 60%.; for the first 6 scenarios sd is kept at current levels (sd=52%) during the high sd window; scenarios 7 and 8, sd is constant at 26% and 52%. finally, the last scenario (yellow) shows a 75% sd (lockdown) with stepping strategy with 40day windows; f) show similar scenarios but with 70% protection; g) show 70% protection and 40% sd; h) show changes in sd through time. 52% with a 30% protection percentage and protection was either 55, 60 or 65% with a 52% sd. world health organization coronavirus disease institute for health metrics and evaluation (ihme). covid-19 projections estimating covid-19 cases and reproduction number in brazil data-based analysis, modelling and forecasting of the covid-19 outbreak so what? risk factor for severity and mortality in adult covid-19 inpatients in wuhan estimate of underreporting of covid-19 in brazil by acute respiratory syndrome hospitalization reports the effectiveness of the quarantine of wuhan city against the corona virus disease 2019 (covid-19): wellmixed seir model analysis high temperature and high humidity reduce the transmission of covid-19 impact of non-pharmaceutical interventions (npis) to reduce covid-19 mortality and healthcare demand projecting the transmission dynamics of sars-cov-2 through the postpandemic period modeling the effects of intervention strategies on covid-19 transmission dynamics wearing facemasks regardless of symptoms is crucial for preventing spread of covid-19 in hospitals google searches for the keywords of "wash hands" predict the speed of national spread of covid-19 outbreak among 21 countries inactivation of severe acute respiratory syndrome coronavirus 2 by who-recommended hand rub formulations and alcohols covid-19) in brazil -statistics & facts to mask or not to mask: modeling the potential for face mask use by the general public to curtail the covid-19 pandemic embassy & consulates in brazil. health alert -some brazilian cities require face coverings the effect of control strategies to reduce social mixing on outcomes of the covid-19 epidemic in wuhan, china: a modelling study beware of the second wave of covid-19 preparing for a responsible lockdown exit strategy herd immunityestimating the level required to halt the covid-19 epidemics in affected countries apmonitor optimization suite. covid-19 optimal control response covid-19-scenarios early spread of sars-cov-2 in the icelandic population estimates of the severity of coronavirus deases 2019: a model-based analysis epidemiologista nao acreditatem subnotificacao de obitos em são paulo 000 missing deaths: tracking the true toll of the coronavirus outbreak world health organization (who) who director-general's opening remarks at the media briefing on covid-19 estimating the final epidemics size for covid-19 nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study the reproductive number of covid-19 is higher compared to sars coronavirus the authors would like to thank apple, cdc, ihme, google and journals that have made data and information relative to covid-19 publicly available. we would also like to thank all the frontline workers risking their lives to help others during the covid-19 pandemic. osmar all authors have discussed, revised and approved the contents of the final manuscript. all authors have agreed to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. the authors declare no conflict of interest. key: cord-268693-td6kvmlq authors: martins, leila droprinchinski; da silva, iara; batista, wellington vinicius; de fátima andrade, maria; dias de freitas, edmilson; martins, jorge a. title: how socio-economic and atmospheric variables impact covid-19 and influenza outbreaks in tropical and subtropical regions of brazil date: 2020-09-16 journal: environ res doi: 10.1016/j.envres.2020.110184 sha: doc_id: 268693 cord_uid: td6kvmlq covid-19 has been disturbing human society with an intensity never seen since the influenza epidemic (spanish flu). covid-19 and influenza are both respiratory viruses and, in this study, we explore the relations of covid-19 and influenza with atmospheric variables and socio-economic conditions for tropical and subtropical climates in brazil. atmospheric variables, mobility, socio-economic conditions and population information were analyzed using a generalized additive model for daily covid-19 cases from march 1(st) to may 15(th), 2020, and for daily influenza hospitalizations (2017-2019) in brazilian states representing tropical and subtropical climates. our results indicate that temperature combined with humidity are risk factors for covid-19 and influenza in both climate regimes, and the minimum temperature was also a risk factor for subtropical climate. social distancing is a risk factor for covid-19 in all regions. for influenza and covid-19, the highest relative risks (rr) generally occurred in 3 days (lag=3). altogether among the studied regions, the most important risk factor is the human developed index (hdi), with a mean rr of 1.2492 (95% ci: 1.0926-1.6706) for covid-19, followed by the elderly fraction for both diseases. the risk factor associated with socio-economic inequalities for influenza is probably smoothed by influenza vaccination, which is offered free of charge to the entire brazilian population. finally, the findings of this study call attention to the influence of socio-economic inequalities on human health. the covid-19 pandemic has been destructive to human lives, economy and social relations around the world. in just a few months, it quickly spread to all countries and killed more than 800,000 people, consuming tens of millions of jobs (worldometer website) . covid-19 is caused by sars-cov-2, which can be transmitted by two main ways: contact (surface contact, i.e. fomites and contact with a contaminated person) and by air, via droplets and aerosol (kutter et al., 2018; patients et al., 2020; setti et al., 2020; stadnytskyi et al., 2020; tellier et al., 2019; world health organization, 2020) . influenza, another respiratory virus, has also caused tens of thousands of deaths worldwide each year. the influenza virus, which can also cause severe acute respiratory syndrome (sars), has forms of transmission similar to although there is no consensus on the relevance of each mode (brankston et al., 2007; killingley and nguyenvan-tam, 2013; krammer et al., 2018; kutter et al., 2018; lee, 2007; tellier, 2006) . therefore, the transmission of both is susceptible to climate conditions and, in the case of influenza, seasonality is already described in the literature (alonso et al., 2007; carleton and meng, 2020; li et al., 2015; moriyama et al., 2020; petrova and russell, 2018; russell et al., 2008; shaman and kohn, 2009; shimmei et al., 2020; sobral et al., 2020) . the world pandemic caused by covid-19 has demanded a huge effort of the scientific community to identify the relevant factors and their associations with virus transmission. as the virus spreads to new areas, more studies are required to understand the disease under the socioeconomic and climate conditions of different countries, especially those in africa and south america (belser, 2020; marson and ortega, 2020; wilder-smith et al., 2020) . besides social distancing, the influence of climate variables on sars-cov-2 spread capacity has already been j o u r n a l p r e -p r o o f explored by some studies (ma et al., 2020; qi et al., 2020; tobías and molina, 2020; xie and zhu, 2020) , as well as other factors (domingo and rovira, 2020; sarmadi et al., 2020; urrutia-pereira et al., 2020) . however, the relations of climate variables were based only on subtropical regions, which makes the pandemic view somewhat early and narrow. even for influenza, only a few studies were conducted in tropical regions and a deep investigation of its relation with environmental variables is still needed (alonso et al., 2007; krammer et al., 2018) . however, such previous studies can provide important insights on , some studies analyzed the influence of temperature, humidity and rainfall (auler et al., 2020; prata et al., 2020; rodrigues et al., 2020; tenório and lansac-tôha, 2020) for some brazilian cities. some factors cannot be ignored to address the spread of respiratory viruses as sars-cov-2 and influenza. for instance, the effects of population age, hygiene measures, social distancing, socioeconomic conditions and climate. therefore, in this study, we investigated the associations of covid-19 cases and the number of hospital admissions by influenza with atmospheric variables, social distancing and socio-economic conditions for different climate regions in brazil. besides, we compare the results of both diseases, aiming to establish a robust relation between influenza and covid-19. brazil is the unique huge country that extends from the equator to the subtropics (5 o 16`19`` n and 3 o 45`07`` s, with an area of 8 516 000 km 2 ) and thus has different climate zones (fig. 1) . the socio-economic conditions also show wide variations inside the country; thus, it is a perfect j o u r n a l p r e -p r o o f area to study the influence of these factors on the dissemination of covid-19 and influenza, two respiratory viruses with similarities in the modes of transmission. in addition, the inherent bias associated with the data record can be minimized using the information of the same country, mainly for covid-19, which is a new disease. another important feature used was to choose regions that do not represent the main gates for people and goods entering the country. the only exception was the state of amazonas, the home of the manaus free trade zone. however, we kept the region in the study, since it is a very particular tropical area, where the main city of manaus is surrounded by the largest tropical forest in the world. the amazonas state has a low population density (2.23 inhabitants km -2 ), but 51% of the population is living in the capital manaus. j o u r n a l p r e -p r o o f five brazilian states representing different climate regimes were chosen (fig. 1) . the state of amazonas (am) has a tropical rainforest climate, with annual average temperature and rainfall of 27.4 °c and 2145 mm, respectively. this type of climate is classified as af (tropical without a dry season), following the köppen climate classification (alvares et al., 2013) . maranhão (ma) and ceará (ce) have a tropical savanna climate, predominantly aw (tropical with a dry winter) and as (tropical with a dry summer), respectively. they have a similar annual pattern of rainfall and temperature, with low-temperature variations during the year, but with well-defined seasonality for the monthly rainfalls. for both states, the rainy season occurs between february and may, while the driest period occurs between august and november. espírito santo (es), located in southeast brazil, has also a tropical savanna climate (aw) in most of its area, but with monthly rainfall not changing significantly over the year, as in ma and ce. there is no welldefined dry season and only a slightly rainy period from november to january. the state of paraná (pr) has well-defined seasons (summer, fall, winter and spring), with humid subtropical (cfa and cfb) oceanic climates, without a dry season. curitiba is the main city of the state, and the average temperature and monthly rainfall are 17.1 °c and 130 mm (climate-data website). the meteorological data were compiled from the national institute of meteorology stations (instituto nacional de meteorologia -inmet, see supplementary material), which consisted of the average daily maximum and minimum temperature (°c), rainfall (mm), relative humidity (%), wind speed (m s -1 ) and insolation (hours), from january 1 st , 2017 to may 15 th , 2020 (inmet website). as the wind speed is not available for all stations, it was not included in the final regression analysis. by the way, no statistical significance was found for this variable in our analysis. should be shared between the three levels of government: federal, state and municipal administrations. however, only the last two moved to do something in their own way, without any coordination or effort from the ministry of health. as a measure of the recognized effect of social distancing on covid-19 dissemination, we used the community mobility reports trends, an indicator provided by google (google covid19 website). this mobility reports show the relative percentual changes in the averaged categorized places concerning baseline days (jan 3 rd -j o u r n a l p r e -p r o o f feb 6 th , 2020), named as mobility. these data present a good linear correlation with a similar product provided by apple. as socio-economic indicators, we used: access to clean water supply, the elderly fraction (≥ 60 years old), and the human development index (hdi) which, in summary, is a measure of three key dimensions related to development: income, education and health. the number of tests performed was also considered in the regression analysis. the indicators were obtained from the brazilian institute of geography and statistics and the ministry of regional development (ibge and snis websites). table 1 shows the values of these variables for each state, besides information concerning the population, case fatality rate (cfr), and the number of intensive care units (icu) available for the studied states. a descriptive analysis of atmospheric variables and health data was performed. a generalized additive model for location, scale and shape (gamlss), combined with the negative binomial distribution, a distribution belonging to the exponential family (hastie and robert, 1990; wedderburn, 1974; stasinopoulos et al., 2018) , were used to investigate the potential influence of the atmospheric and socio-economic variables on covid-19 cases and influenza hospitalizations, as well to determine the most important variables among those analyzed. the model systematic part is given by: where, x ji are the explanatory variables from j=1, 2,…,6; and from time (day) from i=1,…,n: maximum and minimum temperatures, relative humidity, rainfall frequency, insolation and social distancing measured by mobility (only for covid-19). rainfall was added to the model as a binary variable (0 without rain, 1 with rain), since the interest was to observe the effect of its occurrence and not of intensity. hdi is the human development index, water corresponds to the percentage of homes with access to clean water supply in the state, elderly is the fraction of the population aged ≥ 60 years, and test is the number of tests done per 100,000 inhabitants. these variables allowed to observe the scenarios between each studied brazilian state since the socioeconomic and population characteristics are quite variable. after contamination, there is a latency period of the virus in the organism. the incubation period for viruses is quite variable; in general, the interval between exposure and the onset of symptoms varies from 2 to 7 days (lauer et al., 2020; lessler et al., 2009 . therefore, for this study, lags from 0 to 7 days were considered. exposure-response curves were also plotted at lag 3 (3 days of interval between exposure and the onset of symptoms and their notification in this study), using the distributed lag non-linear model (dlnm), with reference values centered on the median of the variable (gasparrini, 2011) . finally, the values of relative risks (rr), at 95% confidence (ci), were calculated for each variable in the states. statistical analyses were performed using the software r 3.6.1 (r core team, 2019). were also those with the highest percentage of relative humidity (mean above 75%). the state of pr, with the lowest temperatures and humidity, presented the most dispersed values for maximum and minimum temperatures. in terms of relative humidity, the greatest dispersion was observed for ma. insolation was significantly higher for pr, around 8 hours, which is almost the double of the average for the other states. the social distancing proposed by the local authorities reduced urban mobility by up to 50%, comparing with the baseline (jan 3 rd -feb 6 th , 2020). the reduction in mobility was not significant, but much worse for am, where the adhesion to social distancing was lower and mobility was reduced by only 20% in the studied period. j o u r n a l p r e -p r o o f probably due to . the cfr values presented in table 1 are higher when compared to statistics reported to other countries (banerjee et al., 2020; verity et al., 2020) . the rr calculated for covid-19 cases is shown in social distancing, measured by mobility changes in this study, also presented a well-marked rr for all states, which corroborates the influence of social distancing measures as recommended by the who and already observed for brazil (aquino et al., 2020; tenório and lansac-tôha, 2020; valenti et al., 2020) . the comparison of the exposure-response curves of mobility and rr at lag 3 is presented in figure 4 . for ce, es, ma and pr, exposure-response curves of mobility and rr present a similar behavior. without any reduction in mobility (100% on the mobility axis of in all states analyzed in this study, a one-week interval was observed between exposure and the onset of covid-19 notifications, but shorter intervals, usually 3 days, were also observed. this time lag estimated here is in the set of variables and it is the interval between the exposure and the notification. the first symptoms after exposure to sars-cov-2 normally occur after 2 to 7 days, but it can extend up to 14 days, which is considered the quarantine time for covid-19 (jiang et al., 2020; lauer et al., 2020) . socio-economic conditions (hdi) proved to be the most important risk factor among the states. this suggests a difficulty for people to understand the importance of hygiene measures and social distancing on the spread of covid-19. in addition, the index indirectly measures the difficulty j o u r n a l p r e -p r o o f that people have to keep social distancing due to the daily need to search for resources for their livelihood. therefore, income and education levels are the main relevant factors. the access to the health care system is another important factor related to socio-economic conditions that can also help explain the high number of deaths in am, ce, and ma, the states with less icu available by inhabitant (see table 1 ). the fraction of elderly, one additional information captured by the hdi, is also an important risk factor, as already noticed and documented by health systems around the world (banerjee et al., 2020; yi-ru wang, 2020; verity et al., 2020) . the elderly are the most vulnerable group to covid-19. the statistical description of atmospheric variables from 2017 to 2019 is presented in the supplementary material (fig. s.3) . the prevalence of influenza hospitalizations (icd j09-j11) is presented in figure 5 . the state of ma presented the highest prevalence of influenza. for ma and ce, a peak of prevalence is observed in march/april, which differs from pr and es, with a peak in may/june, and am, with a peak not clear. the prevalence of influenza in brazil is quite variable, and the fatality rate is 0.4/100,000 inhabitants (for 2019), according to the brazilian ministry of health. this variation is dependent on several factors, including climate conditions, which show wide variations across brazil. influenza presents a well-defined seasonality (fig. 5 and fig. s.4) , as observed for other parts of the world. however, it is not possible to attribute the same association to climate, as observed in other parts of the world. j o u r n a l p r e -p r o o f table 3 presents the influenza rr and ci for the analyzed variables. as mentioned before, the wind speed was previously analyzed, and the results indicate that this variable is not significant. maximum temperature and humidity are the main atmospheric risk factors for hospital admissions by influenza in all analyzed climate regimes. besides, ce and es also presented significant rr for minimum temperature and insolation (protective effect), while pr for rainfall frequency. the results do not indicate hdi as an important factor when comparing the states, although clean water supply is a risk factor, indicating that other socio-economic inequalities should be explored, besides those measured by hdi. an important aspect for all brazilian states is the annual influenza vaccination program of the brazilian unified health system (sus, http://www.saude.gov.br/sistema-unico-de-saude), that provides free influenza vaccine for vulnerable groups (elderly > 60 years old, pregnant women, children under 5 years old, chronic patients, health workers and indigenous population). therefore, the vaccine is a protective factor j o u r n a l p r e -p r o o f for the population, independently of income, which can explain this result for hdi. on the other hand, age is the most important risk factor for influenza, as demonstrated by an rr of 1.7151 (95% ci: 1.6742-1.7574). the set of variables presented a pronounced rr at lag 3 for hospitalization due to influenza, which is in agreement with the latency time for the virus (lessler et al., 2009; o'shea et al., 2019) . the regression analysis performed from march 1 st to may 15 th of years 2017-2019 for influenza provide similar results of those obtained using the total daily data from 2017-2019 (table 3) , with the elderly as the most important factor, with significant rr for temperature and humidity, and no significant rr for hdi (see table s .2). the rainfall and minimum temperature were risk factors in am, which is consistent with the year station and the annual prevalence of influenza. comparing socio-economic characteristics, hdi showed statistical significance for covid-19 and influenza, and amazonas was the state with the highest significance for this variable (see the p-value in table s .3). the percentage of elderly people was statistically more significant in ma for covid-19 while, for influenza, it was pr. in the case of access to clean water supply, the highest statistical significance was observed in the state of ce for both influenza and covid-19. the two states with the lowest number of tests per 100,000 inhabitants, ma and pr, showed higher significance (α = 0.001). hdi and the elderly are important factors for covid-19 cases, while the elderly fraction is remarkably the main factor for influenza in the set of variables and states. as previously argued, this difference may be due to the influenza vaccination provided by sus every year for vulnerable groups. as the vaccine is free and is systematically provided by sus, the existing inequalities measured by hdi are not highlighted in influenza, in an opposite way of what j o u r n a l p r e -p r o o f happens in the case of covid-19, for which no vaccine is available yet. however, other inequalities such as access to clean water supply is a risk factor. temperature and humidity are factors significantly associated with both diseases, which suggests that seasonality may be a factor attributable to both viruses. this explains the high number of cases in the tropical climate. the exposure-response curves for covid-19 and influenza at lag 3 for maximum temperature and relative humidity for am (tropical climate) and pr (subtropical climate) are presented in temperature presents similarities in the risks for covid-19 (fig 6 a and b) and influenza (fig 6 c and d) , with a risk factor above percentile 75 th for both diseases. humidity is also observed in having the same way, as can be seen on exposure-response curves for am (fig. 6) . the same result is observed in the case of pr for both diseases. however, for humidity, these similarities in the curves are not so clear, but the risk is around the mean (tables 2 and 3 ) and a protective factor is observed between 25 th and 75 th percentiles for influenza and 75 th and 99 th percentiles for covid-19. anyway, it is important to note that the covid-19 period in pr presented atypical meteorological conditions (drier) concerning the climatology of the corresponding period. seasonality; temperature and humidity are the main related atmospheric variables. therefore, we believe that covid-19 also has a similar annual cycle like influenza, with tropical regions presenting a different cycle than subtropical regions, since the variability of temperature and humidity is significantly different between these regions. in this study, we evaluated the influence of atmospheric and socio-economic conditions on the spread of covid-19 and influenza in tropical and subtropical states in brazil. covid-19 presented a different epidemiological profile in tropical and subtropical brazilian climates. seasonality showed similarities with the behavior of influenza in previous years. despite the relevance of social distancing, indicated in this study by mobility, the climate had an important influence on both covid-19 and influenza suggesting that, for the tropical region (am, ma, and ce), covid-19 arrived in a favorable time. this favorable climate condition, identified by an abnormal rainy season that influenced humidity, was observed mainly in am and ma and may have contributed to a large number of cases. on the other hand, covid-19 arrived in unfavorable periods and atypical meteorological conditions for pr state, i.e. under much drier and sunnier conditions than normal, with several hours of solar radiation that contributed to the control of covid-19 spread in the state. age is the most important risk factor for influenza, while for covid-19 the hdi is the most important factor to explain the differences among regions in the number of covid-19 cases followed by age and social distancing. j o u r n a l p r e -p r o o f finally, the dataset has limitations associated with sub notifications of cases and deaths by covid-19. similar limitations can be extended to the social distancing measure, analyzed through the mobility changes since it cannot represent with accuracy how far people are staying away from each other. besides, hospital admission for influenza obtained from sus cannot represent the total population, as well as the data available for covid-19 that is yet limited to a few months, which can influence the results. however, we believe that these results can be extended to other similar regions and call attention to the influence of socioeconomic inequalities on the spread of the pandemic. seasonality of influenza in brazil: a traveling wave from the amazon to the subtropics köppen's climate classification map for brazil evidence that high temperatures and intermediate relative humidity might favor the spread of covid-19 in tropical climate: a case study for the most affected brazilian cities estimating excess 1-year mortality associated with the covid-19 pandemic according to underlying conditions and age: a population-based cohort study assessment of sars-cov-2 replication in the context of other respiratory viruses transmission of influenza a in human beings causal empirical estimates suggest covid-19 transmission rates are highly seasonal department of informatics of single system of health effects of air pollutants on the transmission and severity of respiratory viral infections social distancing measures to control the covid-19 pandemic : potential impacts and challenges in brazil 2423-2446 distributed lag linear and non-linear models in r: the package dlnm google covid19. covid-19 community mobility reports. available at the website webpage generalized additive models 1 introduction 2 smoothing methods and generalized addi-tive models does sars-cov-2 has a longer incubation period than sars and mers? routes of influenza transmission transmission routes of respiratory viruses among humans the incubation period of coronavirus disease 2019 (covid-19) from publicly reported confirmed cases: estimation and application transmission of influenza a in human beings incubation periods of acute respiratory viral infections: a systematic review a review of the 2019 novel coronavirus (covid-19) based on current evide identification of climate factors related to human infection with avian influenza a h7n9 and h5n1 viruses in china effects of temperature variation and humidity on the death of covid-19 in wuhan covid-19 in brazil effects of temperature and humidity on the spread of covid-19: a systematic review seasonality of respiratory viral infections viruses associated with foodborne infections, reference module in life sciences 2020. c or r e sp ondence niacin compared with ezetimibe the evolution of seasonal influenza viruses temperature significantly changes covid-19 transmission in (sub)tropical cities of brazil covid-19 transmission in mainland china is associated with temperature and humidity: a time-series analysis regional determinants of the expansion of covid-19 in brazil temperature and latitude analysis to predict potential spread and seasonality for covid-19. ssrn electron association of covid-19 global distribution and environmental and demographic factors: an updated three-month study sars-cov-2rna found on particulate matter of bergamo in northern italy: first evidence absolute humidity modulates influenza survival, transmission, and seasonality association between seasonal influenza and absolute humidity: time-series analysis with daily surveillance data in nacional de informações sobre saneamento, ministério do desenvolvimento regional association between climate variables and global transmission of sars-cov-2 the airborne lifetime of small speech droplets and their potential importance in sars-cov-2 transmission gamlss : a distributional regression review of aerosol transmission of influenza a virus recognition of aerosol transmission of infectious agents: a commentary social distancing and movement constraint as the most likely factors for covid-19 outbreak control in brazil social distancing and movement constraint as the most likely factors for covid-19 outbreak control in brazil covid-19 in brazil: "so what is temperature reducing the transmission of covid-19 ? covid-19 and air pollution: a dangerous association? social distancing measures could have reduced estimated deaths related to covid-19 in brazil estimates of the severity of coronavirus disease 2019: a model-based analysis high temperature and high humidity reduce the transmission of covid-19 updated understanding of the outbreak of 2019 novel coronavirus (2019-ncov) in wuhan quasi-likelihood functions , generalized linear models , and the gauss -newton method can we contain the covid-19 outbreak with the same measures as for sars? modes of transmission of virus causing covid-19 : implications for ipc precaution recommendations association between ambient temperature and covid-19 infection in 122 cities from china the authors would like to acknowledge the organizations and institutes for providing the dataset.we would also like to thank the national council for scientific and technological development (conselho nacional de desenvolvimento científico e tecnológico -cnpq), process grant no. 306862/2018-2. key: cord-281603-3308f8hm authors: souza, william marciel de; buss, lewis fletcher; da silva candido, darlan; carrera, jean paul; li, sabrina; zarebski, alexander; vincenti-gonzalez, maria; messina, janey; sales, flavia cristina da silva; andrade, pamela dos santos; prete, carlos a; nascimento, vitor heloiz; ghilardi, fabio; pereira, rafael henrique moraes; santos, andreza aruska de souza; abade, leandro; gutierrez, bernardo; kraemer, moritz u. g.; aguiar, renato santana; alexander, neal; mayaud, philippe; brady, oliver j; souza, izabel oliva marcilio de; gouveia, nelson; li, guangdi; tami, adriana; oliveira, silvano barbosa; porto, victor bertollo gomes; ganem, fabiana; almeida, walquiria ferreira; fantinato, francieli fontana sutile tardetti; macario, eduardo marques; oliveira, wanderson kleber; pybus, oliver; wu, chieh-hsi; croda, julio; sabino, ester cerdeira; faria, nuno r. title: epidemiological and clinical characteristics of the early phase of the covid-19 epidemic in brazil date: 2020-04-29 journal: nan doi: 10.1101/2020.04.25.20077396 sha: doc_id: 281603 cord_uid: 3308f8hm background: the first case of covid-19 was detected in brazil on february 25, 2020. we report the epidemiological, demographic, and clinical findings for confirmed covid-19 cases during the first month of the epidemic in brazil. methods: individual-level and aggregated covid-19 data were analysed to investigate demographic profiles, socioeconomic drivers and age-sex structure of covid-19 tested cases. basic reproduction numbers (r0) were investigated for sao paulo and rio de janeiro. multivariate logistic regression analyses were used to identify symptoms associated with confirmed cases and risk factors associated with hospitalization. laboratory diagnosis for eight respiratory viruses were obtained for 2,429 cases. findings: by march 25, 1,468 confirmed cases were notified in brazil, of whom 10% (147 of 1,468) were hospitalised. of the cases acquired locally (77.8%), two thirds (66.9% of 5,746) were confirmed in private laboratories. overall, positive association between higher per capita income and covid-19 diagnosis was identified. the median age of detected cases was 39 years (iqr 30-53). the median r0 was 2.9 for sao paulo and rio de janeiro. cardiovascular disease/hypertension were associated with hospitalization. co-circulation of six respiratory viruses, including influenza a and b and human rhinovirus was detected in low levels. interpretation: socioeconomic disparity determines access to sars-cov-2 testing in brazil. the lower median age of infection and hospitalization compared to other countries is expected due to a younger population structure. enhanced surveillance of respiratory pathogens across socioeconomic statuses is essential to better understand and halt sars-cov-2 transmission. the first case of covid-19 was detected in brazil on february 25, 2020. we report the epidemiological, demographic, and clinical findings for confirmed covid-19 cases during the first month of the epidemic in brazil. individual-level and aggregated covid-19 data were analysed to investigate demographic profiles, socioeconomic drivers and age-sex structure of covid-19 tested cases. basic reproduction numbers (r 0 ) were investigated for são paulo and rio de janeiro. multivariate logistic regression analyses were used to identify symptoms associated with confirmed cases and risk factors associated with hospitalization. laboratory diagnosis for eight respiratory viruses were obtained for 2,429 cases. by march 25, 1,468 confirmed cases were notified in brazil, of whom 10% (147 of 1,468) were hospitalised. of the cases acquired locally (77·8%), two thirds (66·9% of 5,746) were confirmed in private laboratories. overall, positive association between higher per capita income and covid-19 diagnosis was identified. the median age of detected cases was 39 years (iqr 30-53). the median r 0 was 2·9 for são paulo and rio de janeiro. cardiovascular disease/hypertension were associated with hospitalization. co-circulation of six respiratory viruses, including influenza a and b and human rhinovirus was detected in low levels. socioeconomic disparity determines access to sars-cov-2 testing in brazil. the lower median age of infection and hospitalization compared to other countries is expected due to a younger population structure. enhanced surveillance of respiratory pathogens across socioeconomic statuses is essential to better understand and halt sars-cov-2 transmission. to investigate individual-level diagnostic, demographic, self-reported travel history, place of residence and likely place of infection, differential diagnosis for other respiratory pathogens, as well as clinical details, including comorbidities, we collected case data notified to the redcap database 8 from february 25 to march 25, 2020. data was contributed by public health and private laboratories. diagnosis and case definitions (see appendix, pp.1) were based on world health organization (who) interim guidance. to explore the time-lag between the number of imported cases and of local cases we used the granger causality test 9 . geospatial analysis of covid-19 cases, demographic and socio-economic data based on data from the first covid-19 reports in brazil 10 , we hypothesized that rates of incidence and testing for covid-19 are higher in areas of higher per capita income. for the greater metropolitan region of são paulo (gmrsp), per capita income at the gmrsp neighbourhood level (517 zones) were retrieved from the 2017 pesquisa origem e destino survey (www.metro.sp.gov.br/pesquisa-od/). 13,913 notified cases (covid-19 confirmed, ruled out, and without final diagnosis) resident in the gmrsp were geocoded based on self-reported address using the galileo algorithm and verified using google api. per capita income for each zone was linked to each notified case based on residential address. we compare per capita income for all notified cases between those tested (positive and negative) and untested, and for confirmed cases by rt-pcr. full details on the statistical analysis can be found in the appendix, pp.1. to quantify transmission potential of covid-19 in brazil, an exponential model was used to represent the incidence of covid-19 at the national level and in são paulo and rio de janeiro states. time series of confirmed cases were modelled as samples from a negative binomial distribution with a mean equal to a fixed portion of the incidence. the analysis was carried out in a bayesian framework with uninformative priors on all parameters apart from the removal rate, which was given an informative prior. the informative prior ensured that the average duration for which an . 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 april 29, 2020. to investigate which factors are associated with a confirmed covid-19 result and with hospitalization summary statistics were calculated for continuous variables and for categorical variables and summarized as medians (range and interquartile range, iqr), as appropriate. missing data were removed (assumed missing at random) (see appendix table s1 and fig. s3 ). uni-and multivariate analysis included only cases with complete information for the relevant variables. these analyses compared demographics, symptoms, clinical signs and comorbidities between confirmed covid-19 cases (rt-pcr positive) and ruled-out covid-19 cases (rt-pcr negative). additionally, separate multivariate logistic regression models were built to predict hospitalisation (binary variable: hospitalised vs. not hospitalised) based on symptoms, clinical signals and comorbidities, and to predict testing status (positive or negative for rt-pcr sars-cov-2). the associations between the outcome and independent variables were reported as adjusted odds ratios (aor) with 95% confidence intervals and likelihood ratio test (lrt) using the univariate and multivariate logistic regression models. model diagnostics were performed to check for model specification errors, multicollinearity and influential observations. a 0·05 significance level was applied. 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 data in the study and had final responsibility for the decision to submit for publication. . 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 april 29, 2020. . https://doi.org/10.1101/2020.04.25.20077396 doi: medrxiv preprint by march 25, 2020, four weeks after the first report of covid-19 in brazil, 67,344 covid-19 cases had been notified as covid-19 suspected infections from 172 cities across all five administrative regions of brazil. of these, 1,468 cases were confirmed (2·18% of all notified cases) and notified through the redcap system (fig. 1a) (fig. 1b) . the epidemic curves of locally-acquired cases followed the curves from imported cases with a lag of two days (granger causality test) (fig. 1a) . 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 29, 2020. . https://doi.org/10.1101/2020.04.25.20077396 doi: medrxiv preprint these locations used a bayesian approach to fit an exponential growth model to covid-19 aggregated incidence data. consistent with previous studies in china and overseas 12 , we find that epidemic spread in são paulo and rio de janeiro states is characterized by similar r 0 values of 2·9 (95% ci 2·1-4·4) and 2·9 (95% ci 2·2-4·5). the r 0 for brazil was slightly higher with median of 3·2 (95% ci 2·4-5·4) (fig. 2) . analysis of the age-sex structure of confirmed and notified cases compared to the brazilian demographic structure revealed a disproportionately lower proportion of confirmed covid-19 infections reported in younger categories (0-9, 10-19 years of age) and a slightly higher proportion in middle-age categories (20-29 and 30-39 years of age) (fig. 3) . specifically, compared to the proportion of the total brazilian population per age category, the proportion of confirmed covid-19 . 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 april 29, 2020. . https://doi.org/10.1101/2020.04.25.20077396 doi: medrxiv preprint infections in the 0-9 and 10-19 years of age categories are 16·4-and 5·3-fold lower compared to brazilian demographic structure (fig. 3a) . we found that most confirmed cases were in males (776 [54·7%] of 1,420 -46 confirmed cases had missing information for sex and/or age) (fig. 3a) . the median age of cases was 39 years (iqr, 30-53, range: newborn-93 years). nearly half (695 [48·9%] of 1,420) of the confirmed cases were in the age range of 20 to 39 years of age (fig. 3a) . similarly, 51·6% (2,288 of 4,438) of cases tested for sars-cov-2 belonged to this age-group (fig. 3b) , which is substantially higher than the corresponding fraction of the brazilian population (68,451,093 [32%] of 211,755,692). 9·5% (133) of cases were health care workers. overall, only four newborns, three infants (6 to 8 month-old), ten children (1 to 12 years old), and twelve adolescents (12 to 17 years old) were diagnosed with covid-19. in addition, nine patients were pregnant, one in the first trimester, one in the second trimester, four in the third trimester and 3 had missing information). six cases were hiv-positive. proportion (%) of the country's population in each age-sex class is shown as faded bars. . 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 april 29, 2020. (fig. 4a) . to test whether notified tested cases were associated with socioeconomic status, we evaluated the association between covid-19 diagnosis and socioeconomic status in the subset of cases in the greater metropolitan region of são paulo (gmrsp) region with geocoded residential information using an ordinal probit model. we found that the proportion of tested cases in gmrsp increased as income per capita increases (z-score = 0.19, likelihood ratio test p-value <0.01) (fig. 4c, table s2 ). moreover, the increase in the proportion of tested cases for a unit-increase in income is higher in weeks 2, 3 and 4 compared to week 1. for the range of income per capita observed, given the same amount of income per capita, the proportions of tested cases were lower in weeks 2, 3 and 4 than week 1. overall, there was a noticeable upwards trend in the association between testing rate and per capita income uncovering a widening socioeconomic disparity in testing practice as the number of cases expands. the income distribution of the untested fraction increasingly approximates the average for gmsp, whereas the tested and confirmed cases (both laboratory and clinical epidemiological) are consistently higher over the study period. we also analysed the results for other respiratory pathogens tested in brazil as part of the differential diagnosis by central public health laboratories and national influenza centres (brazilian , fig. s4 ). . 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 april 29, 2020. in a univariate analysis of4,387 cases with a final classification as confirmed (n=1,101) or discarded (covid-19 ruled out) (n= 3,286), we found that increasing age, symptoms (cough, difficulty breathing, dyspnoea/tachypnea, sputum production, nasal congestion, nasal flaring, nausea/vomiting, headache, irritability/confusion, difficulty swallowing, intercostal retraction and alteration on chest auscultation) and clinical signs (fever and conjunctival congestion) were higher associated with a negative sars-cov-2 results (see appendix table s4 ). overall, a total of 12·5% (184/1,468) of confirmed covid-19 cases had at least one comorbidity. most common comorbidities were heart disease, hypertension, diabetes, and chronic respiratory disease. (figure 5b) . interestingly, age was not significantly associated with hospitalization after accounting for co-morbidities. . 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 april 29, 2020. of the four fatal cases, one had cardiovascular disease/hypertension, one had both cardiovascular disease/hypertension and renal disease, and two fatal cases had no reported comorbidities. only one case had reported close contact with a confirmed covid-19 case reinforcing that local transmission was already well established in brazil by march 25, 2020. . 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 april 29, 2020. . https://doi.org/10.1101/2020.04.25.20077396 doi: medrxiv preprint these findings provide evidence that sars-cov-2 transmission in brazil shifted rapidly from a scenario of imported to local transmission. we found that the proportion of tested cases is higher in zones with higher per capita income. we showed that during the first month of covid-19 in brazil, only 33·1% of the reported confirmed cases were conducted in public health laboratories. our results support similar transmission potential (r 0 ) of sars-cov-2 in brazil to other geographic regions. overall, our clinical findings demonstrate that chest x-ray abnormalities and o 2 saturation <95% are strongly associated with hospitalization. the combination of universal access to diagnostic and the success of interventions will dictate the fate of covid-19 in brazil. overall, these findings 14 . secondly, our retrospective study has focused predominantly on symptomatic patients (92%) that presented themselves to health services for testing. therefore, we cannot describe the full spectrum of disease. population-based serologic surveys are urgently needed to properly determine the asymptomatic and oligosymptomatic fraction. finally, many patients remained hospitalized when the dataset was extracted, and, we were unable to estimate clinical outcomes given the long duration of infection. together with changes in surveillance guidelines, socioeconomic bias in testing suggests that the number of confirmed case counts may substantially underestimate the true number of cases in the population. additional reasons for underreporting include (i) a significant proportion of asymptomatic infections 15 , (ii) people with mild and even moderate disease are unlikely to present to health services for testing, (iii) limited testing capacity in public health service in brazil in face of the large number of cases due to delays in importing reagents and kits used in molecular testing. close monitoring of state-and municipality-level data will further help to inform mitigation strategies. our results suggest that approximately 50% of the covid-19 cases in brazil were skewed towards age groups between 20 to 39 years with substantially fewer cases in younger age groups. this pattern could be explained by (i) a higher risk of exposure of this group due to more frequent international travel (travel bans were only implemented on march 23, 2020), and (ii) younger age . 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 april 29, 2020. . https://doi.org/10.1101/2020.04.25.20077396 doi: medrxiv preprint groups being less likely to acquire an infection and/or less likely to acquire significant symptoms upon being infected 16 . covid-19 infections were reported in paediatric and pregnant patients [17] [18] [19] . paediatric infection appears to typically be of mild or moderate severity; we observed a similar proportion of asymptomatic infections compared to reports in 36 children in china (24% vs. 28%) 19 . also, the onset symptoms of pregnant women were similar to those reported in non-pregnant adults with covid-19 infection. on the other hand, proportion of hospitalisation of paediatric patients in brazil was lower than those observed for children in china (3.3% vs. 38.9%) 19 . also, in contrast to china, none of the pregnant women that tested positive for covid-19 in brazil had pneumonia or were hospitalized 17, 18 . however, the absence/lower number of hospitalisations could be explained by resource availability and local clinical practice guidelines. despite the small sample size, our findings in pregnant and paediatric patients in the early-phase covid-19 pandemic in brazil require further understanding of sars-cov-2 infection in these groups. although clinical features in brazil are similar to those recently reported in other countries 1,4,5 , we observed that 8% of confirmed cases reported no symptoms. this should not be considered as an estimate of the asymptomatic fraction. firstly, it is not possible to distinguish true asymptomatic infections from cases in the pre-symptomatic phase. secondly, routinely collected data tends to be incomplete. thirdly, these cases were tested because they were in contact with a known confirmed case. lastly, there is an ascertainment bias towards symptomatic infections due to the case definition used for notification (appendix). other estimates of the asymptomatic fraction have varied widely, including 18% on the diamond princess ship 15 , 50-75% in the italian village of vo'euganeo 20 and 31% based on repatriation flight screening 21 . overall, 10% of covid-19 cases in brazil were hospitalized compared to 19% in the usa 22 . as mentioned above, these differences may reflect factors other than disease severity, for example, resource availability, local clinical practice guidelines and testing availability. on the other hand, they may also reflect right censoring, whereby cases that were notified towards the end of the period studied had not yet been hospitalized. this would be expected given the median lag of four days between symptom onset and hospitalization observed in brazil. although age was not a risk factor for hospitalization after controlling for comorbidities, is should be noted that the age distribution among patients who were hospitalized differed from that reported in china, with a higher proportion of younger (<39 years: brazil, 24.5% vs. china, 10%) and older patients (>70 years: brazil, 21.8% vs. china, 15%) 18 . however, such comparisons need to be taken cautiously due to different testing and notification practises in the two countries. . 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 april 29, 2020. we showed that patients with pre-existing cardiovascular diseases/hypertension were at increased risk of hospitalization. the prevalence of at least one comorbid condition among infected individuals in brazil was similar to that reported in china (12.5% vs. 10.5%) 23 . previous studies suggest that persons with underlying health conditions, such as cardiovascular, diabetes and chronic lung diseases, appear to be at higher risk for severe covid-19 infection than persons without these conditions 22,24 . pre-existing cardiovascular disease appears to be particularly important, potentially due to the involvement of the renin angiotensin system signalling pathway 25 . this study provides new information on co-circulation and co-detection of other respiratory pathogens in the early phase of the covid-19 epidemic in brazil. particularly, we found cocirculation of eight other respiratory viruses, the most common respiratory infections were influenza a and b, and human rhinovirus (hrv). co-detection of sars-cov-2 with influenza a and human metapneumovirus (hmpv) have also been reported in china 26,27 . here we found co-detection of sars-cov-2 with influenza a and hmpv, and we expanded the description of the other multiple codetection scenarios of sars-cov-2 with other respiratory viruses, including hrv, influenza b, human respiratory syncytial virus, and other coronaviruses (i.e. coronavirus 229e/nl63, hcov oc43/hku1). although, viral co-infection has been reported with many other respiratory viruses, no difference in clinical disease severity between viral co-infection and single infection has been reported 28 . in conclusion, we provide the first description of covid-19 in brazil. our study provides crucial information for diagnostic screening and health-care planning, and for future studies investigating . 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 april 29, 2020. . https://doi.org/10.1101/2020.04.25.20077396 doi: medrxiv preprint clinical features of patients infected with 2019 novel coronavirus in wuhan, china coronaviridae study group of the international committee on taxonomy of v. the species severe acute respiratory syndrome-related coronavirus: classifying 2019-ncov and naming it sars-cov-2 genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding clinical characteristics of coronavirus disease 2019 in china first case of 2019 novel coronavirus in the united states coronavirus disease 2019 (covid-19) in italy world-health-organization. coronavirus disease (covid-2019) situation reports research electronic data capture (redcap)--a metadata-driven methodology and workflow process for providing translational research informatics support investigating causal relations by econometric models and cross-spectral virological assessment of hospitalized patients with covid-2019 the reproductive number of covid-19 is higher compared to sars coronavirus percepção do estado de saúde, estilos de vida e doenças crônicas the lancet infectious estimating the asymptomatic proportion of coronavirus disease 2019 (covid-19) cases on board the diamond princess cruise ship early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia clinical features and obstetric and neonatal outcomes of pregnant patients with covid-19 in wuhan, china: a retrospective, single-centre, descriptive study. the lancet infectious clinical characteristics and intrauterine vertical transmission potential of covid-19 infection in nine pregnant women: a retrospective review of medical records children with coronavirus disease 2019 (covid-19) in zhejiang, china: an observational cohort study. the lancet infectious covid-19: identifying and isolating asymptomatic people helped eliminate virus in italian village international journal of infectious diseases : ijid : official publication of the international society for infectious diseases united states characteristics of and important lessons from the coronavirus the authors thank the clinicians and epidemiologist for technical support. this work was supported key: cord-355800-g1xol1bw authors: favorito, luciano a. title: the new impact factor of international brazilian journal of urology is 1.342. where can we get? date: 2020-09-02 journal: int braz j urol doi: 10.1590/s1677-5538.ibju.2020.06.01 sha: doc_id: 355800 cord_uid: g1xol1bw nan in june 2020 the impact factor of international brazilian journal of urology rises to 1.342. this is the second biggest impact in its history. the journal impact factor is a metric that reflects the yearly average number of citations that articles published in the last two years in a given journal received. the impact factor is very important to the journal importance evaluation. this new impact is due to the hard work of the entire team o int braz j urol and our goal will be to make the int braz j urol impact rise even further and will place the international brazilian journal of urology as one of the five most important in the area at the end of our management. the november-december number of int braz j urol, the 6th under my supervision, presents original contributions with a lot of interesting papers in different fields: prostate cancer, male infertility, renal cell carcinoma, urinary diversion, hypospadia, urinary stones, ureteral cancer, erectile dysfunction, testicular torsion, prostate biopsy, partial nephrectomy, hypospadias and covid-19 in urology. the papers came from many different countries such as brazil, usa, serbia turkey, china, france, italy, india and romania, and as usual the editor´s comment highlights some of them. in the present issue we present three important papers about renal and ureteral stones. dr. wang and colleagues from china performed in page 902 (1) a nice systematic review about the surgical treatments for proximal ureteral stones > 10mm comparing various surgical options such as extracorporeal shock wave lithotripsy (eswl), ureteroscopic lithotripsy (ursl), percutaneous nephrolithotomy (pcnl) and laparoscopic ureterolithotomy (lu) and concluded that lu have the potential to be considered as the first treatment choice of proximal ureteral stone ≥10mm. drs. torricelli and monga from brazil and usa (2) present in page 927 a nice narrative review about the staghorn renal stones and concluded that this stones are most of times composed of struvite and related to urinary tract infection. careful preoperative planning is essential to achieve stone-free status. pcnl is the treatment of choice and auxiliary procedures such as swl and flexible ureteroscopy should be used to treat residual fragments. both prone and supine are effective. the goals of the treatment are the complete absence of kidney stones and eradication of infection with antibiotics and close follow-up is advised with regular imaging exams and urine culture and dr. sahan and collegues from turkey presented in page 1010 (3) a prospective randomized study about the flexible ureterorenoscopy (f-urs) and laser lithotripsy with the new impact factor of international brazilian journal of urology is 1.342. where can we get? _______________________________________________ _______________________________________________ luciano a. favorito 1, 2 regional anesthesia vs general anesthesia and concluded that both general anesthesia and regional anesthesia are equally effective and safe anesthesia methods for f-urs procedures. however, regional anesthesia group showed significantly increased likelihood of bradycardia and mucosal injury during surgery, and significantly decreased surgeon comfort during surgery. the editor in chief would like to highlight the following works too: dr. wang and collegues from china (4) on page 934 evaluated the efficiency of an energy density of 0.05mj/mm2 of low intensity extracorporeal shockwave therapy (li-eswt) on erectile dysfunction (ed) patients and concluded that the energy flux density (efd) of 0.05 of li-eswt could improve the erectile function of ed patients with pde5i response. in addition, efd of 0.05 of li-eswt treatment could turn pde5i non responders to responders. dr. alger and collegues (5) from usa performed on page 962 an interesting study about the impact of obesity on perioperative outcomes and urethral stricture recurrence after anterior urethroplasty and concluded that despite the association with increased urethral stricture length and estimated blood loss, obesity is not predictive of adverse perioperative outcomes or stricture recurrence. obese patients should be offered urethral reconstruction, but patient selection and preoperative counseling remain imperative. dr. dias filho and collegues (6) from brazil performed on page 972 an interesting study about the presentation delay, misdiagnosis rate, inter-hospital transfer times and testicular salvage for testicular torsion patients treated in our state's public health system and concluded that the low overall testicular salvage rates originated from a large proportion of late presentations combined with long transfer times caused by frequent misdiagnoses. the authors results indicate that efforts to improve salvage rates should aim at enhancing population-wide disease awareness and continuously updating physicians working at primary and secondary levels-of-care about scrotal emergencies. dr. sivaraman and collegues (7) from italy developed on page 984 an interesting study about focal therapy (ft) for localized prostate cancer (pca) treatment is raising interest and concluded that hifu ft guided by mri-us fusion may allow improved functional outcomes and fewer complications compared to us-guided hifu ft alone. dr. sefik and collegues (8) from turkey analyzed on page 993 the course of anxiety and depression before and after transrectal ultrasound-guided prostate biopsy (trus-bx) and in the postoperative 1st month when the histopathological biopsy result was obtained and concluded that pre-biopsy anxiety disappeared after bx, but there was a significant increase in anxiety and depression in patients after the diagnosis of malignancy. dr. zidde and collegues from brazil (9) performed an interesting translational study on page 1021 (the cover paper in this number) about the arterial segments of ovine kidney and analyze arterial injuries caused by simulated partial nephrectomy of cranial pole. the authors concluded that the segmental distribution of renal artery, the proportional volume of each segment and arterial injuries after cranial pole resection in ovine kidneys are different from what is observed in human kidneys. meanwhile, ovine kidneys show a primary segmental division on anterior and posterior, as in humans, but different from swine. these anatomical characteristics should be considered when using ovine as animal models for renal experimental and/or training procedures. dr. bandinni and collegues from serbia, romania, india and italy (10) performed on page 1029 evaluated the feasibility of vacuum physiotherapy meant to decrease graft contraction and recurrent penile curvature (pc), hence successful tubularization and a straight penis in patients underwent two--stage buccal mucosa graft (bmg) urethroplasty, in proximal hypospadias repair and concluded that physiotherapy with the vacuum device is safe, easy and practically feasible. our vacuum physiotherapy protocol had high compliance rate. vacuum physiotherapy should be considered for further assessment in patients undergoing two stage hypospadias repair using buccal mucosa. dr. gomes and collegues from brazil (11) on page 1042 evaluated the impact of covid-19 on clinical practice, income, health and lifestyle behavior of brazilian urologists during the month of april 2020 and concluded that covid-19 produced massive disturbances in brazilian urologists' pracunidade de pesquisa urogenital da universidade do estado de rio de janeiro -uerj, rio de janeiro, rj, brasil e-mail: lufavorito@yahoo.com.br efficacy and safety of various surgical treatments for proximal ureteral stone ≥10mm: a systematic review and network meta-analysis staghorn renal stones: what the urologist needs to know flexible ureterorenoscopy and laser lithotripsy with regional anesthesia vs general anesthesia: a prospective randomized study low intensity extracorporeal shockwave therapy shifts pde5i nonresponders to responders larger patients shouldn't have fewer options: urethroplasty is safe in the obese presentation delay, misdiagnosis, inter-hospital transfer times and surgical outcomes in testicular torsion: analysis of statewide case series from central brazil does mpmri guidance improve hifu partial gland ablation compared to conventional ultrasound guidance? early functional outcomes and complications from a single center anxiety and depression associated with a positive prostate biopsy result: a comperative, prospective cohort study anatomical background of ovine kidney for use as animal model: analysis of arterial segmentation, proportional volume of each segment and arterial injury after cranial pole partial nephrectomy vacuum physiotherapy after first stage buccal mucosa graft (bmg) urethroplasty in children with proximal hypospadias impact of covid-19 on clinical practice, income, health and lifestyle behavior of brazilian urologists the gud technique: glandar urethral disassembly. an alternative for distal hypospadias repair http://orcid.org/0000-0003-1562-6068 int braz j urol. 2020; 46: 689-90 tice, with major reductions in patient visits and surgical procedures. distressing consequences were also observed on physicians' income, health and personal lives. these findings are probably applicable to other medical specialties.dr. macedo and collegues from brazil (12) performed on page 1072 an amazing alternative procedure for distal hypospadias consisting of urethral mobilization and partial glandar disassembly, namely gud (glandar urethral disassembly) technique and that this operation can be regarded as a genuine alter-native to distal hypospadias (coronal and subcoronal) but should not be addressed to midshaft forms.the editor-in-chief expects everyone to enjoy reading and for sure better times will come soon. key: cord-103179-naynznc1 authors: simon, l. m.; rangel, t. f. title: are temperature suitability and socioeconomic factors reliable predictors of dengue transmission in brazil? date: 2020-11-04 journal: nan doi: 10.1101/2020.11.02.20224444 sha: doc_id: 103179 cord_uid: naynznc1 background dengue disease is an ongoing problem, especially in tropical countries. like many other vector-borne diseases, the spread of dengue is driven by a myriad of climate and socioeconomic factors. over recent years, mechanistic approaches have predicted areas of dengue risk according to the temperature effect on mosquitos' lifespan and incubation period shaping their persistence and competence in transmission. within developing countries such as brazil, heterogeneities on socioeconomic factors are expected to create variable conditions for dengue transmission by its main vectors. however, both the relative role of socioeconomic aspects and its association with the temperature effect in determining the effective dengue prevalence are poorly understood. methodology/principal findings here we gathered essential socioeconomic factors comprising demography, infrastructure, and urbanization over 5570 municipalities across brazil and evaluated their relative effect on dengue prevalence jointly with a previously predicted temperature suitability for transmission. using a simultaneous autoregressive approach (sar), we showed that the variability in the prevalence of dengue cases across brazil is highly explained by the combined effect of climate and socio-economic factors. moreover, the temperature effect on transmission potential might be a better proxy at some dengue epidemy seasons but the socioeconomic factors are tightly linked with the recent increase of the dengue prevalence over brazil. conclusions/significance in a large and heterogeneous country such as brazil recognizing the drivers of transmission by mosquitoes is a fundamental issue to effectively predict and combat tropical neglected diseases as dengue. ultimately, it indicates that not considering socioeconomic factors in disease transmission predictions might compromise efficient strategies of surveillance. our study indicates that sanitation, urbanization, and gdp are regional indicators that should be considered along with temperature suitability for dengue transmission, setting a good starting point to effective vector-borne disease control. 12 background 13 dengue disease is an ongoing problem, especially in tropical countries. like many 14 other vector-borne diseases, the spread of dengue is driven by a myriad of climate and 15 socioeconomic factors. over recent years, mechanistic approaches have predicted areas 16 of dengue risk according to the temperature effect on mosquitos' lifespan and 17 incubation period shaping their persistence and competence in transmission. within 18 developing countries such as brazil, heterogeneities on socioeconomic factors are 19 expected to create variable conditions for dengue transmission by its main vectors. 20 however, both the relative role of socioeconomic aspects and its association with the 21 temperature effect in determining the effective dengue prevalence are poorly 22 understood. 23 here we gathered essential socioeconomic factors comprising demography, 25 infrastructure, and urbanization over 5570 municipalities across brazil and evaluated 26 their relative effect on dengue prevalence jointly with a previously predicted 27 temperature suitability for transmission. using a simultaneous autoregressive approach 28 (sar), we showed that the variability in the prevalence of dengue cases across brazil is 29 highly explained by the combined effect of climate and socio-economic factors. 30 moreover, the temperature effect on transmission potential might be a better proxy at 31 some dengue epidemy seasons but the socioeconomic factors are tightly linked with the 32 recent increase of the dengue prevalence over brazil. 33 in a large and heterogeneous country such as brazil recognizing the drivers of 35 transmission by mosquitoes is a fundamental issue to effectively predict and combat 36 tropical neglected diseases as dengue. ultimately, it indicates that not considering 37 socioeconomic factors in disease transmission predictions might compromise efficient 38 strategies of surveillance. our study indicates that sanitation, urbanization, and gdp are 39 regional indicators that should be considered along with temperature suitability for 40 dengue transmission, setting a good starting point to effective vector-borne disease 41 control. 42 43 author summary: 44 dengue, a disease transmitted by mosquitoes, is a great problem in countries 45 where the climate is predominantly hot and wet. researchers know that temperature 46 plays an important role in mosquitoes' ability to transmits diseases. usually, 47 temperature alone is a good explanation for why dengue occurs in certain regions that 48 have stable warm temperatures. here we show that, in addition to the role of 49 temperature on dengue spread, large urban areas with sanitation infrastructure and 50 health assistance also prelude dengue cases prevalence. we highlight that dengue 51 surveillance should consider socioeconomic regional differences. for instance, greater 52 urban centers might be the focus of the dengue burden, where the presence of medical 53 assistance and sanitation seems not to avoid the increase in disease cases. conversely, 54 less urbanized regions with suitable temperature for dengue transmission might require 55 distinct actions for the disease combat. 56 57 . 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 november 4, 2020. ; https://doi.org/10.1101/2020.11.02.20224444 doi: medrxiv preprint the presence and prevalence of many infectious diseases have clear geographic 59 structures. these health threats vary from country-to-country and cause the loss of 60 millions of lives annually (1,2). identifying patterns and drivers of infectious diseases 61 spread has become a fundamental concern on disease ecology (3). for instance, 62 understanding why some regions have a higher charge in diseases and pathogens 63 richness than others might help to identify hotspots for infections outbreak (2). 64 however, a multitude of factors determines infectious disease geographical distribution 65 and potential outbreaks, spanning from socioeconomic (e.g. urbanization; population 66 density) to environmental (e.g. temperature; precipitation) and biotic (e.g. vectors 67 competition) aspects (1,4). acknowledging the variation over space in these drivers of 68 infectious disease is increasing among ecologists in an attempt to identify regions of 69 outbreak potential, once the disease dynamic is as tightly linked with exogenous factors 70 as it is with endogenous mechanisms (5,6). 71 dengue, a mosquito-borne infectious disease, is a global public health concern. 72 the incidence of dengue has increased thirty-fold over the last five decades, and it is 73 estimated that approximately one hundred million new infections occur annually (7). in 74 the americas, the disease is present in almost all countries with great prevalence (8), 75 where rapid urban expansion led to ideal environmental conditions for dengue to spread 76 (9). nonetheless, dengue is still considered a neglected tropical disease (10). the 77 geographic distribution of dengue vectors and the probability of virus transmission to 78 human hosts are likewise driven by the ecological role of temperature (9,11). despite its 79 pervasiveness, the effect of ecological variables like temperature and precipitation 80 might be outweighed by the influence of socio-economic aspects on dengue 81 . 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 november 4, 2020. ; https://doi.org/10. 1101 /2020 reproduction and development (16, 20) . in this sense, some infectious diseases prevail 106 in countries where the characteristics of both demography and infrastructure create 107 favoring conditions for transmission outcomes (12). 108 distinct approaches have been used to address the presence and prevalence of 109 infectious diseases, such as mechanistic (i.e., process-based) and statistical models 110 a multi-model climate-driven approach has also been proposed to forecast aedes-borne 118 diseases and support surveillance operations (25). albeit integrating many transmission-119 related factors might turn intractable in a process-based procedure, the absence of key 120 drivers still brings uncertainty to the estimated transmission potential (24). 121 although dengue is present in almost all tropical and subtropical countries (7), 122 brazil has experienced a higher-than-expected number of infection cases in the last 123 century (8,10). since the 80's, the reintroduction of dengue in the country has led to its 124 rampant geographic expansion (26). initially the presence of dengue virus was more 125 intense in large urban centers, but since 90's it has spread to small towns and 126 countryside. in the 2000s, the dengue vectors (i.e., aedes aegypti and aedes albopictus) 127 were already present in 72% of brazilian municipalities, dramatically increasing the 128 disease cases and overloading the brazilian health system (27). although pervasive 129 . 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 november 4, 2020. ; https://doi.org/10. 1101 /2020 across brazil, the prevalence of dengue cases varies widely among the urban centers 130 making it difficult for dengue season preparedness especially in conjunction with other 131 infectious disease outbreak (27, 28) . 132 in this paper we evaluate the relative impact of socioeconomic conditions and 133 temperature suitability over the spatial pattern of dengue fever prevalence across brazil. 134 we used a previously estimated temperature suitability for dengue transmission (23) 135 and 7 socio-economic variables to study the prevalence of dengue disease in 5570 136 municipalities across brazil. we also seek to understand the fit between the estimated 137 temperature suitability for transmission and the effective prevalence of dengue in the 138 last years. we predict that in a highly heterogeneous country, such as brazil, 139 socioeconomic factors are the greater source of high levels of dengue prevalence. in 140 brazil, regions with the highest dengue prevalence are not those with highest estimated 141 temperature suitability for transmission, although suitability is still a good indicator of 142 the disease occurrence. 143 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 november 4, 2020. ; https://doi.org/10.1101/2020.11.02.20224444 doi: medrxiv preprint clinical and epidemiological evidence, and are carried out by a local health surveillance 152 team (30). 153 (ii) temperature suitability 154 here we used the simulated dengue transmission suitability maps by brady et al. 155 (23) as a predictor of dengue presence and prevalence in brazil, from which we extracted 156 the raster information regarding each municipality. brady et al. (23) , estimated the 157 dengue transmission suitability from the temperature influence on mosquitoes' (ae. 158 aegypti and ae. albopictus) survivorship and extrinsic incubation period (i.e., eip). the 159 eip represents the period between mosquito biting an infected host and being able to 160 transmit the virus after processing the pathogen into the gut (i.e., become infectious) 161 (31). brady's et al. (23) mechanistic model considered the dynamic between the eip and 162 the adult vector survival -both temperature-dependent -over the basic reproductive 163 number (i.e., r0) (see (32,33)). the model outcome was then combined with a spatially 164 explicit temperature data, producing predictive maps of vectors' suitability range on the 165 persistence and competence of dengue transmission (23). 166 for each brazilian municipality, we likewise gathered important socio-economic 168 predictors to the distribution and prevalence of mosquito-borne diseases (see table a 169 in s1 appendix), which were: human population density, urbanization, population size, 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 november 4, 2020. ; https://doi.org/10.1101/2020.11.02.20224444 doi: medrxiv preprint political-administrative extension comprises 5570 municipalities, which were all 174 included. 175 epidemiological studies suggest that regions with high population density and 176 great urbanization favor the increase of dengue cases by facilitating vectors' mobility 177 and reproduction (20,36). here we estimated the population density as the ratio among 178 population size and the area of each municipality. we accounted for the population size 179 as the total number of people within each municipality, following the ibge classification. 180 to access the proportion of urbanization within municipalities, we estimated the ratio 181 between the urbanized area (maps based on satellite images (34)) and the whole 182 political-administrative extent from each municipality. also, to account for the effect of 183 medical diagnosis, notification and local investments, we used the number of people 184 assisted by educational and health assistance in each municipality (16, 27) . finally, to 185 represent economic development, we also considered gdp (log scale) and the presence 186 of the basic sanitation system (i.e., sewage treatment and/or rainfall water 187 management) (see table a in s1 appendix). 188 we employed linear correlations among the predictor variables to assess their 190 collinearity. in a stepwise procedure, we evaluated the non-independence between the 191 predictors by measuring the variance inflation factor (vif) among them and set apart 192 the most redundant variables. we started with a full model and iterated the procedure 193 until all the predictors had a vif lower than 10 (37). according to this procedure the 194 variables population size and education are the most collinear and were therefore 195 removed from analyses. although important to disease transmission in general (table a 196 . 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 november 4, 2020. ; https://doi.org/10. 1101 /2020 in s1 appendix), the population size has a confounding relation with gdp in brazil as a 197 consequence of internal migration patterns to economically developed areas (38). 198 because our analysis is spatially explicit, we accounted for the spatial 199 autocorrelation that could potentially inflate type-i errors of statistical inferences (39). 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 november 4, 2020. dengue cases are unevenly distributed across brazil, both in occurrence and 221 prevalence (i.e., number of cases) (fig 1) . over the last years, most dengue cases showed 222 to be concentrated into the southeast and midwest regions of brazil, but were also less 223 frequently present in the north and northeast. from 2007-2014 (fig 1a) there were 224 fewer recorded dengue cases when compared with a more recent epidemic period 225 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 november 4, 2020. ; https://doi.org/10.1101/2020.11.02.20224444 doi: medrxiv preprint circles corresponds to the magnitude of dengue prevalence (i.e., the mean number of cases). the intensity 233 of purple indicates the mean temperature suitability for the dengue transmission by aedes spp. vectors 234 (23). the graphical comparison between the distribution of real dengue cases (fig. 1, 236 red circles) and the estimated temperature suitability for potential dengue transmission 237 ( fig. 1, purple shades) the autoregressive model revealed that the relative importance of the socio-248 economic factors and estimated temperature suitability for dengue transmission in 249 brazil (table 1) 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 november 4, 2020. ; https://doi.org/10.1101/2020.11.02.20224444 doi: medrxiv preprint transmission also showed higher explanatory power for the distribution of dengue cases 257 in 2007-2014 (z = 14.825) than in 2015-2016 (z = 7.145 human population density was not a significant explanatory factor for the 261 number of recorded dengue cases in both periods, neither was its interaction with 262 estimated temperature suitability for dengue transmission. however, urbanization, a 263 proxy for the expansion of human-modified areas, was found to be an important 264 . 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 november 4, 2020. ; predictor of the dengue cases from 2007 to 2014 (table 1) . both urbanization itself and 265 its interaction with the temperature suitability for dengue transmission were significant 266 in those previous years, but less relevant in the more recent period of 2015-2016. the 267 coefficients of determination (r 2 ) of the sarerror models varied between periods, 268 suggesting that the same socio-economic variables and the temperature suitability for 269 dengue transmission have higher explanatory power during years of lower transmission 270 (r 2 = 0.53) than in periods of an increased outbreak (r 2 = 0.49). the sar model had lower 271 aics than its ordinary least squares (ols) counterpart (table 1) . 272 spatial autocorrelation was successfully controlled by the sar model (fig a in s2 273 appendix). the residuals of the models revealed a narrow variation on the range of 274 values and there were no marked spatial patterns of residuals across brazil (fig 2) . in the 275 southern region the residuals are very small in many municipalities, indicating that 276 model predictions were accurate in these areas. in contrast, some municipalities in the 277 amazon region had negative residuals (overestimated number of dengue cases), 278 whereas some municipalities in central and southeast brazil had positive residuals 279 (underestimated number of dengue cases) (fig 2) . 280 . 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 november 4, 2020. ; https://doi.org/10.1101/2020.11.02.20224444 doi: medrxiv preprint the higher prevalence of dengue over brazil compared to other countries has 285 intrigued researchers for decades, revealing that singular factors might regulate the 286 transmission of this infectious disease within particular countries (27). this constant 287 reemergence and maintenance of a high number of dengue cases in brazil remain 288 unclear, which is justified due to the complex nature of the biological features of virus 289 (e.g., serotypes, virulence), host (e.g., immune system) and vectors (e.g., ambient 290 suitability, reproduction rates) (45). therefore, the magnitude of the dengue incidence 291 fluctuates according to a myriad of environmental factors. our results showed that, 292 although temperature suitability for transmission is a good indicator of dengue 293 . 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 november 4, 2020. ; https://doi.org/10.1101/2020.11.02.20224444 doi: medrxiv preprint occurrence, the socio-economic characteristics are the fundamental determinants of 294 the spatial patterns in dengue prevalence in brazil. 295 similar to other tropical nations, brazil is a heterogeneous country that has 296 undergone substantial urban growth in recent decades. this rapid urban expansion 297 along with favorable climatic conditions creates an ideal scenario for the establishment 298 and spread of critical infectious diseases, especially those carried by mosquitoes (22). 299 however, dengue occurrence and number of cases differ substantially among regions 300 within brazil. thus, predicting the potential transmission of mosquito-borne infectious 301 disease requires incorporating environmental and socio-economic heterogeneities 302 among regions, especially in countries where an endemic scenario is well established 303 (27) . although the temperature is a physical factor known to affect the physiology of 304 mosquitoes and its capacity as disease vectors (18) 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 november 4, 2020. ; https://doi.org/10.1101 https://doi.org/10. /2020 temperature scenarios. under lower spatial and temporal scales, the relationship 318 between temperature and multiple other drivers, such as urbanization, gdp, and 319 sanitation, should be more appropriate to describe patterns of disease transmission 320 (16, 18) . for instance, we showed that brady's et al. model 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 november 4, 2020. ; https://doi.org/10.1101/2020.11.02.20224444 doi: medrxiv preprint sanitation system and gdp with the prevalence of dengue, indicating that their presence 342 by itself may not attest to the benefits of economic wealth in reducing the dengue 343 disease cases in brazil. 344 the demography in urban environments is thought to be an important driver of 345 dengue prevalence (50). for instance, a temporal analysis of the dengue outbreak in 346 singapore found that the population demography is the main driver for the dengue 347 increase in the last years (51). this encounter is usually accurate given the expected 348 mixed contact between hosts and vectors, where the pure increase in individuals density 349 is expected to increase the contact rates between hosts and vectors (32). however, after 350 controlling for other covariates, our model did not find a substantial effect of 351 demography on the prevalence of dengue cases across brazil. although demography 352 might be a good proxy for the number of susceptible individuals, in dengue-endemic 353 countries such as brazil the serotypes immunization is likely to reduce this proportion 354 (52). still, the population density may have great importance at the local scale (e.g., 355 among neighborhoods), once it increases the probability of vector contact with hosts 356 when the virus is installed (53). the greater relation of municipalities' gdp with dengue 357 prevalence could also be an indication of the interchange between higher population, 358 immunization, and different serotypes circulating, once brazilian cities with greater 359 income grown faster by historically being attractive for migration (54). 360 there is no doubt that the burden of dengue is heavier in some regions than 361 others. in brazil, where dengue cases greatly vary across space and time, we highlight 362 that the combined effect of climate and socio-economic factors drive the dengue 363 occurrence and prevalence. still, due to the lack of reliable reports on dengue 364 prevalence, most predictive models overemphasize the role of temperature on dengue 365 . 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 november 4, 2020. ; https://doi.org/10. 1101 /2020 transmission in large scales (22). by accounting for the effect of socio-economic drivers 366 in an extremely heterogeneous country, we showed that dengue prevalence is 367 explained not only by the temperature suitability for transmission but also by social and 368 economic factors. highly urbanized centers with great income were found to be 369 epicenters of dengue transmission in brazil, aligned with other infectious diseases (55). 370 consequently, projections of dengue risk areas over actual or future climatic conditions 371 should include socioeconomic covariates to make predictions reliable for decision 372 making regarding a vector-borne tropical neglected disease such as dengue, especially 373 when considering that dengue season might come when another infectious disease 374 epidemic is already overloading the health system (e.g. sars-cov-2). here we 375 emphasize the need of considering social, economic, and cultural differences between 376 brazilian regions for effective decision making. 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 november 4, 2020. ; https://doi.org/10. 1101 /2020 supporting information 531 532 s1 appendix. 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 november 4, 2020. ; https://doi.org/10. 1101 /2020 disease ecology, biodiversity, and the 390 latitudinal gradient in income. hochberg me, editor ecology drives the worldwide 393 distribution of human diseases the neglected geography 395 of human pathogens and diseases global drivers of human pathogen 397 richness and prevalence 399 relationship between altitude and intensity of malaria transmission in the usambara 400 mountains, tanzania temperature modulates dengue virus epidemic growth rates through its effects on 403 reproduction numbers and generation intervals who. world health organization dengue -paho/who | pan american health organization dengue reborn: widespread resurgence of a resilient vector the 412 global distribution and burden of dengue 414 modelling adult aedes aegypti and aedes albopictus survival at different temperatures in 415 laboratory and field settings lifestyle limits transmission of dengue virus. emerg infect dis joint effects of climate variability and 422 socioecological factors on dengue transmission: epidemiological evidence the ecology of climate change and infectious diseases review of the factors modulating dengue transmission global spread and persistence of dengue traits, behavior, and disease transmission systematic variation in the temperature 434 dependence of physiological and ecological traits regulation and stability of host-parasite population 437 interactions: i. regulatory processes et 439 al. climate, environmental and socio-economic change: weighing up the balance in 440 vector-borne disease transmission 443 the many projected futures of dengue global temperature constraints on aedes aegypti and ae. albopictus persistence and 446 competence for dengue virus transmission consensus and conflict 448 among ecological forecasts of zika virus outbreaks in the united states aedes: a next-generation monitoring and forecasting system for 452 environmental suitability of aedes-borne disease transmission. sci rep expansion of the dengue transmission area in brazil: the 455 role of climate and cities dengue: twenty-five years 457 since reemergence in brazil sã£o paulo urban heat islands have a higher incidence of dengue than 460 other urban areas dengue 465 and dengue hemorrhagic fever, brazil the incubation periods of dengue viruses. vasilakis n, 468 editor infectious diseases of humans: dynamics and control. 470 oup oxford; 1992 modelling the global constraints of temperature on transmission of plasmodium 473 falciparum and p. vivax. parasit vectors a 479 global assembly of adult female mosquito mark-release-recapture data to inform the 480 control of mosquito-borne pathogens a caution regarding rules of thumb for variance inflation factors internal migration and economic development in brazil spatial autocorrelation and the selection of simultaneous 487 autoregressive models 489 spatial dependence: weighting schemes nagelkerke njd. a note on a general definition of the coefficient of 495 determination the global distribution of the arbovirus vectors aedes aegypti and ae. albopictus. 502 elife climate change 504 could shift disease burden from malaria to arboviruses in africa. lancet planet health local and global effects of climate on 507 dengue transmission in puerto rico potential 509 distribution of dengue fever under scenarios of climate change and economic 510 development 512 population density, water supply, and the risk of dengue fever in vietnam: cohort study 513 and spatial analysis social behavior and demography drive patterns of fine-scale dengue transmission in 521 endemic areas of colombia. paul r, editor. plos one history, epidemiology and diagnostics 524 of dengue in the american and brazilian contexts: a review epidemiological and clinical characteristics of the covid-19 epidemic in brazil. nat 528 hum behav key: cord-335578-u8b66oos authors: simões e silva, ana cristina; oliveira, eduardo a.; martelli, hercílio title: coronavirus disease pandemic is a real challenge for brazil date: 2020-06-05 journal: front public health doi: 10.3389/fpubh.2020.00268 sha: doc_id: 335578 cord_uid: u8b66oos nan in december 2019, a cluster of pneumonia cases of unknown etiology was reported in wuhan, china (1). on january 7, a novel coronavirus was identified from the throat swab sample of a patient (2) , and by january 2020, the virus had been isolated and sequenced (3) . the new virus was subsequently named sars-cov-2/human/wuhan/x1/2019 (sars-cov-2) (4). on march 11, 2020 , the who announced that the disease caused by sars-cov-2, designated covid-19, should be considered a global pandemic (5). by may 03, 2020, there were already 3,349,786 confirmed cases of contamination and 238,628 deaths throughout almost the whole world (6) . this first pandemic of the twenty-first century places unprecedented pressure on societies and healthcare systems around the world. as pointed out by jones in a recent commentary, "a history of epidemics offers considerable advice, but only if people know the history and respond with wisdom" (7) . approximately 56 days after the first case reported in china, on february 26, brazil officially registered its first patient with covid-19: a 61-year-old man living in são paulo who had recently returned from a trip to italy. twenty days after the first reported case (march 17, 2020), brazil registered the first death by covid-19 in a 62-year-old man with diabetes and heart disease (8). on march 30, 2020, brazil recorded 4,470 confirmed cases and 159 deaths. by may 25, 2020, brazil had already experienced 363,211 confirmed cases and 22,666 deaths by covid-19 (https://covid. saude.gov.br/). however, it should be noted that these numbers underestimate the real depth of the pandemic in brazil. this is because, to date, capacity for a massive surge in laboratory testing has not been enabled in our country (9) . in this respect, to decentralize the diagnosis of coronavirus, institutes linked to the ministry of health have become responsible for training 27 central public health laboratories on testing, starting in february 2020. since march 18, central public health laboratories from 26 states and the federal district have been considered able to perform tests for coronavirus. nevertheless, in this regard, to date, the country is far below the optimal number of tests for covid-19, as there are not enough tests to achieve a reliable panorama of the real number of cases. currently the rate in brazil is only 14.5 tests/million as compared with the rates of >70 in italy and the uk, for example. the distribution of the resident population according to age group shows a downward trend in the proportion of people <30 years old along with an increase in the proportion of older people. in 2012, people below 30 years old represented 47.6% of the population. this proportion decreased to 42.9% in 2018, while the proportion over 30 years old increased to 57.1% (10) . moreover, chronic diseases, especially systemic arterial hypertension and diabetes mellitus, and their related morbidity and mortality are currently a prevalent public health issue. data from the ministry of health show that the prevalence of hypertension and diabetes among brazilian adults aged 35 and older was 24.3 and 11.7%, respectively. the rates are higher in people aged over 65, in whom the prevalence rises to 54.9 % for hypertension and 19.3% for diabetes. with the rapid spread of covid-19, by the end of march, the main brazilian states had adopted a series of social distancing measures. these included recommending that older adults and individuals with chronic medical conditions stay at home as much as possible, canceling mass events, closing schools, universities, and workplaces, and maintaining only essential services (8) . furthermore, the ministry of health is hiring 5,811 emergency physicians, particularly in poorer cities and indigenous villages, to work to control disease spread. the collapse of healthcare systems is the major concern for most countries hit by the pandemic, especially low-and middle-income countries, such as brazil. for instance, among the confirmed cases in china, 18.5% were considered severe, and 25.3% of those required intensive care. among 4,103 covid-19 patients in new york, 1,999 (48.7%) were hospitalized, and 445 patients (10.8%) required mechanical ventilation (11) . therefore, a critical aspect of the covid-19 pandemic is healthcare system capacity. since 1989, brazil has established a universal public health system (sus, sistema único de saúde) that, in this current pandemic scenario, allowed a coordinated response among the diverse federation units (12) . however, our capacity to deal with critical cases is limited and very heterogeneous across the 26 states. in brazil, the number of intensive care units (icus) through february 2020 amounted to 36,939 beds, according to the cadastro nacional de estabelecimentos de saúde (cnes), with a historical occupancy of not <85%, which yields an ∼5500 free icu beds. the global european number of icus per 100,000 inhabitants is ∼10, with the us leading the world with a ratio of 34.7:100,000; both, however, are far below what is expected to be needed as the number of infections approaches its peak (13) . in the absence of any efficient treatment and/or vaccine to impede the fast spread of the disease, many public policies and governmental strategies, termed nonpharmaceutical interventions (npis), have been used amid the epidemic/pandemic situation. currently, many such public health measures involve reducing social contact in the population and, consequently, the transmission rate of the virus, alleviating the pressure on the health system and providing time for auxiliary measures to be put in place (expansion of the system, creation of military hospitals, and so on). in this regard, another critical aspect is the difference in population adherence to social isolation measures in the different cities and states of the country (14) . it is worth mentioning that all of these measures have critical socioeconomic and ethical implications because they severely interfere with the outflow of industrial products and commodities, reduce spontaneous social aggregations, and so on. therefore, to lift these drastic measures after the control of the initial wave, which is expected to demonstrate exponential growth in the number of confirmed cases, the who has recommended that isolating, testing, and treating every suspected case and tracing every contact must form the backbone for every country's response. this is the best hope for preventing widespread community transmission. most countries with sporadic cases or clusters of cases are still in a position to do this. many countries are following the who recommendations and finding solutions to increase their ability to implement the full package of measures. in summary, the brazilian challenge is not only to stop the spread of covid-19 but also to find agreement between political leaders, scientific societies, and the general population. the brazilian scientific community and healthcare workers are working hard to provide support for political health measures to address covid-19 (15, 16) . hopefully, this pandemic may be an opportunity for political leaders and the general population to clearly comprehend the pivotal importance of science and the public health system in their daily lives. in this regard, a recent editorial highlighted the difficulty of imagining a world that has not been permanently changed by covid-19 (17) . thorp , the editor of science magazine, considered that the success of the world's scientists, along with strong political and social leadership, will determine which scenarios unfold, so it is time to focus on what we can all do to help (17, 18) . thus, the only way to deal with pandemics is with solidarity and cooperative measures from political leaders, scientists, healthcare providers, and the general population. as, eo, and hm collected data, wrote the paper, and aprroved the final version. all authors contributed to the article and approved the submitted version. outbreak of pneumonia of unknown etiology in wuhan, china: the mystery and the miracle epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study a pneumonia outbreak associated with a new coronavirus of probable bat origin the species severe acute respiratory syndromerelated coronavirus: classifying 2019-ncov and naming it sars-cov-2 who. coronavirus disease 2019 (covid-19) situation report -104 history in a crisis -lessons for covid-19 the impact of early social distancing at covid-19 outbreak in the largest metropolitan area of brazil a model to predict sars-cov-2 infection based on the first three-month surveillance data in brazil. medrxiv available online at factors associated with hospitalization and critical illness among 4,103 patients with covid-19 disease in new york city. medrxiv covid-19 in brazil: advantages of a socialized unified health system and preparation to contain cases datadriven study of the covid-19 pandemic via age-structured modelling and prediction of the health system failure in brazil amid diverse intervention-strategies. medrxiv covid-19 mathematical model reopening scenarios for são paulo -brazil. medrxiv underreporting of death by covid-19 in brazil's second most populous state. medrxiv socio-demographic caracteristics and prevalence of risk factors in a hypertensive and diabetics population: a cross-sectional study in primary health care in brazil thorp hh. stick to science the authors of this opinion article are funded by the minas gerais state research foundation-fapemig, minas gerais, brazil, the national council for scientific and technological development -cnpq, brazil, and the coordination for the improvement of higher education personnel, capes, brazil. 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 simões e silva, oliveira and martelli. 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-344639-t9xbzczc authors: devore, jonathan title: from sharecropping to equal shares: transforming the sharing economy in northeastern brazil date: 2020-08-09 journal: dialect anthropol doi: 10.1007/s10624-020-09603-4 sha: doc_id: 344639 cord_uid: t9xbzczc concepts of sharing and commons are normatively and historically ambivalent. some forms of sharing, such as sharecropping or alms-giving, proceed from and sustain asymmetrical relations to the means of life. access to commons in other social contexts merely serves to make unequal forms of life more bearable. in other words, some expressions of sharing and commons are “functional” within hierarchical societies. departing from these observations, this contribution traces contests over the logic of sharing, and apportioned shares of common land, from brazil’s slave period through contemporary land rights movements in the northeastern state of bahia. for former slaves and their descendants, “freedom” often meant sharecropping on the same plantations from which they had been released. however, rural brazilians have also succeeded in transforming shared land into more equal and equitable distributions, from “peasant breaches” that emerged in slave gardens from the early colonial period through the abolition of slavery, to land occupations that occurred in the late twentieth century. by sharing land and other material resources—especially tree seeds, seedlings, and cuttings—rural laborers have established unexpected reconfigurations in distributions of property and social recognition that exceed institutionalized norms of sharing common land. with such outcomes in view, this contribution distinguishes socially replicative and transformative sharing. ongoing economic restructuring, new enclosures, and the erosion of social protections into the twenty-first century continue to sunder people's access to and control over means for sustaining life (bartels 2008; orser 2012) . meanwhile, the means of life themselves are threatened by the undeniable consequences of climate change, and the looming specter of the infelicitously named "anthropocene" (see malm and hornborg 2014; moore 2017 moore , 2018 . 1 these circumstances compel us to reexamine old and new forms of distribution, while reconsidering our relation to the means of life as mere means; for that upon which we are radically dependent can hardly be mere. as we rethink key concepts and ideas, the familiar and well-worn political antinomies of the past century (e.g., individualism and collectivism, private and collective property) will no longer serve us (devore 2017b); that ideological field of correlated but apparently opposed concepts served parallel logics of accumulation over the twentieth century that contributed to the destruction of human and other nature (foster 2015) . as we reconstruct core political practices and institutions, concepts such as sharing and commons have become catchwords among activists, while drawing renewed attention among scholars (benkler 2004; helfrich and bollier 2015; widlok 2017) . the so-called sharing economy has become especially important as the majority of the world's human population now lives in condensed urban and peri-urban areas, where the finitude of human lives and lifeworlds becomes strikingly evident. innumerable smartphone apps enable people to share rides, appliances, housing, baby clothes, labor, and so forth. these sharing economies give new life to the circulation of old things, help renews bonds of trust, and foster economies of care. at the same time, however, the rise of the sharing economy can also be viewed as a mark of diminishing incomes and the neoliberal dismantling of the welfare state (cockayne 2016; martin 2016; morton 2018) , such that "much of what goes under the label sharing economy is in fact not sharing at all," but rather a "euphemism" for and "mystification of commercial market relations" (widlok 2017:140) . these brief remarks suggest that concepts of sharing and commons are normatively and historically ambivalent apart from their historical specifications in social practice, with varied emancipatory outcomes. in a classic piece on egalitarianism among east african foraging societies, woodburn characterized norms of sharing as preventing the emergence of social inequalities through foreclosure on saving, investment, and accumulation. in such contexts, sharing had the effect of "disengage [ing] people from property, [and] from the potentiality in property rights for creating dependency" (woodburn 1982:445) . sharing was thus one among several political tools-a "levelling mechanism" (widlok 2005 )-that people in these communities could employ to either flatten or otherwise prevent the emergence of social hierarchies. in societies where property is a salient and organizing principle, by contrast, sharing may occur among those with unequal access to, and control over, means of life. the english commons that were enclosed over the sixteenth and eighteenth centuries were, indeed, functional aspects of larger manor systems and integral to feudal society. the practice of "gleaning," for example, involved common rights that supervened upon, but did not cancel, the titles of feudal lords. while commoners sometimes violently defended the common "usages" that made life for them bearable (thompson 1993) , these same social arrangements-viewed within their larger context-helped to sustain the lives of the commoners' counterpart, the english aristocracy. john locke variously described england's aristocrats as "lazy and indigent people," whose "debauchery" and "expensive vanity" led them to "waste" resources through "extravagant expenses" (locke 1824 [1691 ]:53, 71-73, cited in ashcraft 1986 . in feudal russia, in the years leading up to (and even after) the 1861 emancipation edict, the "commune" (mir, obshchina) system of land ownership similarly served to make life bearable for serfs and peasants who were subject to numerous forms of extraction by russia's landed elites (waldron 2007:61) , while the commune organization itself served as a vehicle through which up to one-third of their production was extracted (moon 1999:77) . 2 commons and communes in such contexts, in other words, were not separate from the world of feudal lords and aristocrats; commons were rather a reflection of, and embedded within, an unequal and hierarchical society. in such sociohistorical contexts, and in stark contrast with the kind of sharing economy described by woodburn, sharing and commons both proceeded from and reaffirmed differences between society's "haves" and "have-nots." it was for reasons such as these that immanuel kant-who was so thoroughly invested in the enlightenment project of exploding hierarchically ascribed status distinctions-was opposed to alms-giving. giving alms and charity reflected and reproduced the hierarchical status of giver and receiver, meanwhile sustaining the distinction between them (allais 2015 , cited in ferguson 2015 cf. sypnowich 2006) . along these lines, i consider this kind of sharing replicative sharing, insofar as it tends to replicate (or reproduce) the form of society from which it arises. by contrast with forms of sharing that merely reproduced unequal societies, kant instead endorsed the gradual leveling of status distinctions, such that the difference between what he characterized as "active" and "passive" citizens would eventually dissolve (kant 1999 (kant [1797 :119-121; see ladd 1999:xlviii-xlix) . this leveling could occur through state-led reforms designed to redistribute those material goods and resources necessary for their active inclusion in the citizenry (dodson 2003) . along these lines, i consider this kind of sharing transformative sharing, insofar as it tends to transform (or reconstruct) the form of society from which it arises. 3 different logics of sharing thus either presuppose or entail different visions of society and the good, producing different outcomes for distributive and recognitive justice. for this reason, as i suggested above, concepts of sharing and commons are ambivalent apart from their historical and institutional specifications. but it is also not enough to look to institutional specifications of sharing or commons, for those explicit logics are not coextensive with the full range of unanticipated consequences that may emerge from experimental or even routinized patterns of sharing, whether in actual or historical social practice. some forms of sharing may be unexpectedly replicative, while others may be surprisingly transformative. in this contribution, i explore unexpected social 2 in the important volume, late marx and the russian road, teodor shanin (1983) cites an editorial in a journal published by the social revolutionary party of the people's will, which describes the decadence of the mir in 1879: "such too is the situation of the mir. for what purpose does the mir, the obshchina, exist? with what does it concern itself? supplying recruits, collecting taxes, recovering arrears, forwarding contributions in kind-that is the life of the mir. and just as the peasant loses his individuality in an enforced pursuit of the rouble, so too does the obshchina lose its identity and become distorted, stifled by the regime in this sphere of exclusively fiscal and police obligations" (cited in shanin 1983:220-221) . 3 the distinction i suggest between "replicative" and "transformative" sharing is broadly informed by nancy fraser's (1995) distinction between "affirmative" and "transformative" distributive politics, which i have recently employed elsewhere to explore the transformative potentials of conditional cash transfer programs and redistributive land reform politics in brazil (devore 2019). i would prefer the term "reproductive" instead of "replicative"; however, the former term carries unintended connotations in gender ideologies that associate women's labor with reproductive labor. consequences that occurred internal to sharing economies in the northeastern brazilian state of bahia, drawing analytic insight from g.w.f. hegel's (1977 hegel's ( [1807 ) critique of feudal property relations in the phenomenology of spirit. in the few paragraphs on the so-called dialectic of "lordship and bondage," hegel draws our attention to ways that the routinized performance of social hierarchy, and asymmetrical distributions of property and personhood, may activate critical normative intuitions about self, society, and justice. i elaborate this theoretical framework further below after describing the ethnographic and historical context in brazil. in my presentation and analysis of the evidence, i focus on plots of land on the margins of brazilian plantations, in provision grounds called roças. in such provision grounds, and across historical contexts, enslaved africans prior to 1888 and free plantation laborers throughout the twentieth century were permitted to cultivate garden crops for their own subsistence-and sometimes sale in local markets. such provision grounds bear a "family resemblance," in wittgenstein's (1953) sense, to feudal commons briefly described above, as they are embedded within larger landholdings and productive arrangements that make life bearable for commoners but are otherwise controlled by social elites. beyond shared land, however, i also focus on other economies of shared seeds, labor, and even car rides, which were substantially reconfigured as land rights organizations that emerged in bahia in the 1990s directly challenged the asymmetrical distribution of land. this contribution draws on long-term field research with diverse land rights movements in the cacao zone along the southern coast of bahia, brazil, which appeared in the 1990s near the rural towns of ituberá and camamu (see fig. 1 ). these social movements express broader, multigenerational struggles to overcome the enduring legacies of chattel slavery and the reinscription of bondage-or what some rural brazilians call "captivity" (cativeiro) (devore 2014:366-367, 534-535)-to wage labor in the decades following legal emancipation after 1888. the historical arc of this research ranges from a reconstruction of the post-emancipation lifeworld built by poor rural families in this region's hills, followed by violent land grabs and dispossessions that forced these families back to plantation life and labor between the 1950s and 1970s. the story culminates with a surge of land occupations that occurred in the region between the late 1980s and 1990s. one key limitation that freed slaves faced in brazil's post-emancipation period involved the asymmetrical distribution of land, which favored an elite class of large property owners. because of the maldistribution of land, many former and legally freed slaves were compelled to work as wages laborers and sharecroppers, often on the same plantations from which they had been released (fraga filho 2016; mahony 1996) . those families that refused plantation labor, however, took to the forests and hills of southern bahia, including the municipalities of ituberá and camamu, where they sought to reconstruct their lives (fraga filho 2016:101). since 2002, i have been conducting ethnographic and ethnohistorical research in this region, totaling 38 months of fieldwork. on the basis of oral histories, i sought to reconstruct the lives of the free families inhabiting the region's forests and hills prior to the 1950s (devore 2014:26-293), which complements earlier and more recent research by other scholars who help develop a fuller picture of the region's history (flesher 2006; rocha da silva 2018) . historically, this region exhibited both the physical and social characteristics of what scott (2009) calls a "hill space," or what beltrán (1979) described as a "region of refuge." dense forest cover, heavy rainfall, steep hills, and waterways with limited navigability, historically converged to forestall the emergence of a robust plantation economy in this micro-region. indeed, earlier in the nineteenth century, this region was home to escaped slaves who formed mocambo or quilombo communities (schwartz 1992:104-109) . in the decades following abolition, freed slaves, their families, and other members of the rural poor built a social world in these hills characterized by democratized control over land and an ethos of mutual aid (devore 2014:77-158). they succeeded, at least in some measure, in creating a world apart from the forms of subjection and coercive dependency that persisted on plantations elsewhere in bahia. leeds (1957:37) and tosta filho (1948) in the post-war period from the 1950s through the 1970s, however, these families were subjected to processes of "primitive accumulation" (marx 1976 (marx [1867 ), or "accumulation by dispossession" (harvey 2003) , as plantation capital encroached on the region. families living in the hills were forcibly removed from the land, their houses were burned, and they either departed for hinterlands elsewhere, or else turned to wage labor on plantations that were being established in the region. one of brazil's most infamous capitalists, the late norberto odebrecht , was a key player in dispossessing local families and helping to establish new rubber and cacao plantations by the 1970s (devore 2017a, 2018). by the 1990s, however, the land claims of local plantation owners were contested by land rights movements that emerged in the wake of a fungal disease that was introduced to the region in the late 1980s (pereira et al. 1989 )-a witch's broom fungus (crinipellis perniciosa) that devastated the cacao plantations. plantation laborers who were laid off as a result of this crisis joined together and formed diverse land rights organizations. these included decentralized squatter organizations formed by former plantation laborers who occupied abandoned plantation lands; independent associations that sought to directly purchase plantation lands from former owners; and brazil's internationally known social movement, the landless rural workers' movement, or mst. in the region around ituberá and camamu, these different groups occupied more than a half-dozen plantations (devore 2014 (devore , 2015 . this history points to a broad, multigenerational struggle for emancipation and economic freedom that was occurring well before, and long after, the culmination of legal emancipation in brazil in 1888. emancipation was not a legislative act (or even a collection of legislative acts in brazil's case), but a long and abiding labor on the various material and symbolic conditions of people's lives. one of the sites for this ongoing work of emancipation has proceeded through the reconstruction of a sharing economy in which mere access replicated and reaffirmed social hierarchies that were grounded in asymmetrical distributions of land ownership. across historical periods, tensions that emerged internal to hierarchical arrangements of land sharing gave rise to unexpected reconfigurations in distributions of property and personhood, pointing toward possibilities of sharing on a more equal footing. in the following sections, i characterize ways that sharing land was both functional within, and replicative of, plantation hierarchies, while simultaneously bringing about unanticipated leveling effects. from the sixteenth century through the abolition of slavery in 1888, it was common practice in brazil, and indeed throughout the americas, for slave-owning planters to provide their slaves with plots of land where they could grow their own food provisions (berlin and morgan 1991; genovese 1974:535-540; schwartz 1992:49-55) . these plots, referred to as roças in brazil, were usually located on marginal plantation lands where valuable cash crops, such as sugar or coffee, could not be profitably cultivated (barickman 1994) . the term roça derives from the verb roçar, which refers to the process of clearing and opening new plots of land for cultivation. clearing a roça in southern bahia involved difficult and dangerous work, as it meant felling large trees to clear small patches of forest. some nineteenth century bahian sugar planters suggested that provision grounds could obviate the need to provide sustenance for their enslaved labor force, with some planters suggesting that slaves should be given "a day instead of a ration" (calmon 1834, cited in barickman 1994:663, emphasis in original). 4 by this expression, calmon referred to planters who believed that slaves should be given a day off from plantation labor, usually on sundays, to cultivate their own roças. in these plots, and under their own direction, enslaved families could plant subsistence crops such as beans, corn, various vegetables, and manioc. manioc tubers were processed into a coarse flour, called farinha de mandioca, that was and remains a key component of rural bahians' diets. the purpose of providing slaves with land to plant for themselves was twofold, both functional and instrumental. in the first place, as these provision grounds permitted slaves to provide for their own subsistence, slave owners could reduce or eliminate the need to provide food rations to their slaves. for the planter class, provision grounds provided an economical way to cut costs and increase profits. the second rationale for providing slaves with provision grounds was ideological control (silva 1989) , which resonates with arguments about the disciplining effects of labor, and specifically the act of making objects for the enjoyment of others, elaborated in g.w.f. hegel's dialectic of "lordship and bondage" (1977[1807] :118). as the nineteenth century planter miguel calmon noted: [a] master should give his slave some property or make it easier for him to acquire some on his own and should encourage his industry. this is a powerful means of distracting him from the ideas that go hand in hand with his sad condition and of inspiring in him a desire to work and even of inviting him to form a family. the practice of encouraging him to plant a roça, especially with food crops, of allowing him to have some livestock or to exercise some trade-this without doubt will lead to his happiness since it can modify the unruly tendencies that slavery generates and fosters. [calmon 1834:60, cited in barickman 1994:681] calmon thought that providing slaves with plots of land, as well as the time to work for themselves, helped sustain the plantation as an enterprise while serving to replicate plantation society. however, the disciplining effects of labor do not only reproduce the relationship between master and slave. the complex relation between labor, property, and emancipation is crystallized in hegel's critique of german feudal society, which provided the historical backdrop for his famous account of landed "lordship" (grundherrschaft) and "bondage" (or serfdom; knechtschaft) (see cole 2004 )-the so-called master-slave dialectic. 5 hegel's core insight was that the routinized performance of roles institutionally ascribed to master and slave give rise to unintended, transformative, and emancipatory consequences, especially with respect to the slave's institutional status, as such. whereas the master's orientation to the objects upon which the slave labors-which for the master were defined by their "simple sensuous qualities"was merely that of a "desiring-consuming subject" (redding 2012:53) , the slave's orientation to those same objects is mediated in several, more complex ways. first, to successfully produce the object, the slave cannot merely act on immediate impulse, but must defer any consumptive desires; second, she must act according to a concept of the thing she produces; third, her work on the object is socially mediated by the will of another, on whose behalf she acts (see redding 2012:53-56) . in short, the slave's lifeworld is far more multifaceted, complex, and socially developed than the profoundly impoverished worldview of the master. analytic philosopher paul redding describes the consequences in the following way: this mediation means that while the slave is addressed by the master as a slave, and so recognizes himself in that address as a slave, there are other relations that can contribute to the form of self-consciousness of which the slave is capable, relations that can allow the slave to recognize himself in ways that come into contradiction with his self-identity as a slave. [redding 2012:55-56] . in other words, through her work, the slave grasp herself as something more than a "slave," as there are inferential (i.e., semiotic) consequences of her work that disrupt, contradict, and exceed the social status that is ascribed and available to her. the relationships in and through which people variously shape and transform the world activate latent normative intuitions about property, distributive justice, and social recognition; the seemingly lowly activity of laboring on things thus becomes a critical source for renewed self-awareness-along the path toward what marx envisioned as a revolutionary society (see taylor 1975:154-157 )-with corrosive effects on asymmetrical (and institutionally sanctioned) distributions of property and personhood. as an organization of labor, the consequences of provision grounds in brazil were much further reaching than the purposes explicitly envisioned by brazilian slave owners, leading to what historians and historically attentive anthropologists have described as a "peasant breach" in the institution of slavery itself (cardoso 1979 (cardoso , 1988 see barickman 1994; mintz 1974; schwartz 1977) . 6 historians have examined postmortem estate inventories to infer consequences of the customary rights that emerged through the peasant breach. in the southern recôncavo, just south of salvador and north of bahia's cacao zone, barickman reported on an 1857 inventory that listed "a coffee grove that had once belonged to a slave named joaquim ('outra porção de cafezeiros que foram do escravo joaquim') with an appraised value of rs.15$000" (1994:661). in bahia's cacao zone, mahony cites an inventory dated to 1849, listing 84 cacao trees, ten years old at the time, as being "without value because they belonged to joão, a slave on the fazenda [plantation]" (1996:350). these cases suggest that, through planting cacao and coffee trees, enslaved people such as joão and joaquim were able to create specifiable, legally recognizable, and defensible property rights on land that was shared with them by plantation owners. independent of the slave owners' intended purposes, enslaved brazilians were able to create and stabilize shares of their own that garnered both de facto social recognition and later de jure, legal recognition. these social facts, proceeding from cultivated roças, militated against slaves' legal and institutional roles as mere property objects. having secured small spaces of autonomy within the plantation landscape, and opportunities to accumulate small bits of wealth for themselves, these peasant breaches even helped some slaves to achieve their freedom through "self-purchase." 7 whereas in the cases described by woodburn, sharing had both the purpose and effect of dissolving social hierarchies by foreclosing opportunities to generate and accumulate property, in southern bahia, slave owners' decisions to provide slaves with plots of land they could cultivate for themselves had a similar (if incipient) effect on dissolving social hierarchies. by contrast with the context that woodburn described, however, this leveling effect operated through a generalized opportunity to generate and accumulate property among slaves, who were otherwise the objects of others' claims to ownership and mastery. by accumulating property for themselves, slaves could contest and subvert the property claims of their masters. in other words, the customary practice of sharing marginal plots of plantation land with enslaved laborers brought about gradual and subtle internal reconfigurations within bahia's plantation and slave economy. in slavery and social death, orlando patterson (1982:28) wrote the following about slaves in societies where the "personalistic idiom" of slavery was predominant: "the slave was a slave not because he was the object of property, but because he could not be the subject of property." in brazil, enslaved people demonstrated that they were more than mere objects of others' property, precisely through their emergence as subjects of property. this was hardly an intended outcome of this particular institution of land sharing, at least as it was conceived by the class of slave-owning planters in brazil. in the post-emancipation period after 1888, and throughout the twentieth century, it remained a common practice for brazilian planters to permit free wage laborers to cultivate provision grounds on plantation properties, which continued to be referred to as "roças." as before, these provision grounds mingled workers' interests with those of the plantation owners and managers. on the rubber and cacao plantations that emerged near ituberá and camamu in the 1950s, plantation owners permitted workers to cultivate both subsistence and cash crops of their own on plantation lands, including beans, corn, manioc, and certain-but not allvarieties of bananas. 8 for workers, manioc and bananas served the dual purpose of providing sustenance as well as potential cash flow through their sale in local markets. in return for access to these provision grounds, and after their crops were harvested, the workers would restore these plots of land to the landowners. in some agreements, workers had to either leave the land prepared for re-cultivation by the plantation, or else deliver their roças planted with cash crops that would belong to the plantation. in other words, workers' subsistence gardens had to eventually be converted into a form of living capital for the plantations, such as in the form of cacao groves or pasture grass. these land-sharing arrangements benefitted workers and landowners in different ways. workers could provide for their subsistence and sell any surplus on local markets. landowners, on the other hand, received newly cultivated plots of land without expending any capital (e.g., in wages), as the costs of preparing land for cultivation, including the heavy work of clearing forest, were assumed entirely by the workers. in short, workers' labor was converted directly into productive capital for the plantation. these modern provision grounds thus amounted to a windfall for landowners, reproducing processes of labor extraction and capital accumulation, while ultimately leaving the asymmetrical distribution of capital in land intact. in other words, sharing plots of uncultivated land with workers served to replicate both plantation production and the asymmetrical form of society. certain forms of cultivation, however, were proscribed in these modern provision grounds. above, i referred to the enslaved laborers, joão and joaquim, who held property in the cacao and coffee trees that they planted on their masters' lands. in the twentieth century, rural workers who cultivated trees-rather than beans, manioc, or vegetables-or built any other durable infrastructure on plantation lands could similarly make claims to property rights that interfered with the rights of landowners. one young man named silvano, a resident at a squatter community called nossa senhora, recalled this when he suggested that, at least historically, cacao planters prohibited workers from keeping any cacao seeds. these seeds could be used as instruments of "reverse" dispossession against the landowners-much like in the cases of the enslaved laborers, joão and joaquim. against these prohibitions, silvano explained, plantation workers could swallow handfuls of seeds while harvesting them from cacao pods and smuggle them out of the plantation in their bellies. after defecating the seeds, they could plant them in small cacao groves of their own, which one day might help the workers free themselves from plantation labor. unlike beans and manioc, cacao and other trees formed a durable presence on the land where they were planted, and thus staked durable claims to the land itself upon which they persisted. for this reason, sharing and planting certain kinds of seeds was thus proscribed, as such seeds could threaten the distribution of property in land. in other words, sharing certain kinds of seeds threatened plantation production, and the asymmetrical form of society, by potentially freeing workers from their dependence on wage labor. nonetheless, the cultivation of other fruit trees could form part of a worker sharing economy within the plantation landscape. a plantation worker named caio thought it was beneficial to cultivate fruit trees on plantation grounds, as these could form part of a sharing economy among workers residing on the plantations. when workers cultivated fruit trees near worker housing, caio explained, then any and all future workers to inhabit such housing would share in an abundance of fruit for their subsistence. planting fruit trees on plantation grounds thus amounted to an expression of solidarity among the workers themselves. a former plantation worker named damião, now a squatter at nossa senhora, explained that jackfruit (artocarpus heterophyllus) trees were a common resource that provided nourishment for people and many other organisms, he explained, as it benefits "me, a person doing odd jobs [fazendo bico], birds." because such trees were a public good, damião felt that it was "a crime to cut down a jackfruit tree." despite their undeniable good, however, such common resources do not threaten the asymmetrical structure of society, but rather help to make life bearable for those on the margins. indirectly, these forms of sharing help to replicate plantation production and plantation society. as was already suggested above, however, the cultivation of certain kinds of durable tree crops posed risks for landowners. a man named colodino, a former plantation worker who eventually settled at nossa senhora, explained that many plantation managers prohibit workers from cultivating any kind of tree varieties, as trees are what is commonly referred to as bens de raíz. the concept of a bem de raíz (singular; bens de raíz, plural) is an old term common to portuguese and brazilian jurisprudence, which literally translates as "root good." a root good refers to any form of immovable property (immóvel), and may include buildings, any improvements or additions to existing buildings, structures such as fences or drying ovens, or any other durable modification to the biophysical and built environment that is not (easily) moveable elsewhere. in southern bahia, trees also count as root goods. the expression "root good" has obvious botanical overtones, and in the language of rural families and plantation workers, root goods primarily refer to trees and other perennial plants. manioc, although literally a root crop, is not a root good because its presence on the landscape is relatively fleeting and impermanent. colodino explained that root goods may thus include things like: in other words, if a worker (or squatter) plants trees on plantation land, and does so with their own labor, resources, time, and volition-rather than as part of a work agreement or contract with another landowner-then those trees become the personal private property of the person who planted them. 9 because such property is durable on the landscape, with roots literally entangled with another's property in land, landowners may either be required to compensate workers for those trees' monetary values, or else effectively cede their control of the land. 10 as i have described elsewhere, this was precisely what happened with a woman named alvina, who created property of her own by planting trees on land controlled by her miserly in-laws (devore 2018:512 and 2014:235-238, 563-566) . shared space on plantation lands, consequently, was often limited by the kinds of things that could be safely cultivated, at least from the perspective of plantation owners. less durable annual crops like beans, corn, tomatoes, and manioc could be safely cultivated, as the physical space to which their presence staked a de facto claim had a limited time horizon. tree crops such as rubber or cacao, however, posed distinct risks as they threatened to convert the properties of large landowners into the properties of workers. in the second half of the twentieth century, as occurred with the provision grounds owned by slaves, practical understandings about "root goods" were increasingly codified. following the military coup in 1964, the brazilian government passed a series of agrarian legal reforms that were meant to placate and demobilize the peasant leagues that were gaining momentum in northeastern brazil (pereira 1997) . these reforms included the 1964 land statute (estatuto da terra), one effect of which was to bolster rural workers' ownership claims to any improvements or other durable modifications they made on the plantations where they resided and worked. 11 in a study of workers' syndicates in the state of rio de janeiro, o'dwyer (2008) suggested that the "land statute guarantees workers, who planted bens de raíz on garden plots [sítios] located on large properties, the [legal] condition of owner over the improvements made" (2008:237, my translation). without proper indemnification, root goods could not be alienated from the workers who created them. 9 caio and colodino make apparently contradictory claims. in their statements briefly examined above, caio suggested that it both good and even commonplace for workers to plant fruit trees near worker housing, whereas colodino suggested that plantation owners and managers generally prohibit the cultivation of any root goods. the difference probably lies in the degree to which different plantation owners and managers found it worthwhile to micromanage their properties, and to root out each and every clandestine grove. the key difference, however, probably lies in the negligible market value for tree fruits meant for immediate consumption in contrast with the market value of tree crops, such as cacao or cupuaçu. 10 the possibility of losing control and ownership of one's property is related to another legal concept called "usucaption," which brazilian civil law inherited from roman civil law via the portuguese, and is alive in local language. usucaption is a form of "prescriptive acquisition" or "adverse possession." the latin term usucapio (to capture, or take possession, by continuous use and enjoyment), or usucapião in portuguese, is sometimes rendered by local squatter families as "usu-campeão," which could be translated as "use champions," analogous to victors in a soccer match. the cultivation of trees on another's land would provide evidence for continuous use and enjoyment necessary to win such a contest. 11 law no. 4.504 of november 30, 1964. the cultivation of durable trees, or any other root goods, reappeared as a legally codified action through which rural workers could make and stake property claims for themselves. land sharing economies negotiated among plantation owners and laborers during and prior to the twentieth century thus exerted pressure on legal systems such that they aligned with noncodified social practice. for this reason, certain forms of land sharing were increasingly proscribed, as they threatened the overall distribution of access to and control over land. sharing land with workers to plant beans, corn, and manioc made only minor concessions to, but ultimately reaffirmed, the unequal society. planting trees or any other durable crop, however, threatened to destabilize (if not overthrow) the hierarchical edifice. the land occupations that occurred between the mid-1980s and 1990s in bahia's cacao zone amounted to an even more radical transformation of the region's political and moral economy. instead of the gradual, and often implicit, transformations of land and property relations that occurred through different peasant breaches on plantation lands, the land rights organizations that emerged in the region at the end of the twentieth century made stronger and more direct claims to land of their own. as squatter organizations took up and occupied plots of land for themselves, their claims threatened the hierarchical social order, including previous forms of clientelistic social exchange that characterized relationships between plantation owners and workers. the claims advanced by different land rights organizations were thus met with violent reactions from local land-owning elites. a former plantation called angústia was one of the first to be occupied in the hills west of ituberá and camamu. the occupation there began in the mid-to late-1980s, and was protracted, conflicted, and violent. damião, who participated in that occupation before eventually settling at nossa senhora, recalled the occupation: "a lot of people died there, lots of people died in that invasion. gunmen killed lots of people, and the people killed lots of gunmen." a squatter at angústia named ulisses recalled the fear that he and his companions felt whenever they walked down rural roads in the early years of the occupation. "when we heard a car [approaching], we had to dive hidden into the bushes," for they feared the arrival of hired gunmen and thus for their lives (cf. devore 2014:624-634). honório, another squatter at angústia, recalled that local landowners "treated us as invaders. they never offered rides to nobody...they wanted nothing to do with [não queria meia] with the people, not even to say 'good day.'" honório's phrase, "they didn't want nothing to do with the people" (não queria meia com o povo) initially refers to the denial of social recognition, such as in the refusal to say "good day" (bom dia). but the phrase "nothing to do," from the portuguese expression não querer meia, is more accurately translated as "they didn't want half" or a "share" with the people, as the term meia also recalls the practice of sharecropping (produçao de meia). thus, it is significant that honório mentions landowners' collective refusal to offer people rides, or what is referred to as a carona in brazil. ride-sharing between rural workers and vehicle-owning landowners is a common manifestation of clientelistic social exchange in bahia's cacao zone, and throughout brazil more generally. ride-sharing is an asymmetrical form of exchange, a favor that cannot be returned, insofar as many (if not most) landless rural workers do not own vehicles of their own, and thus lack opportunities to reciprocate. although these asymmetrical acts of ride sharing cannot be reciprocated, a return can nonetheless be achieved by expressing deference to and esteem for the person who gave the ride. reminding others of one's previous acts of ride sharing, and calling attention to one's generosity, can be used to make those others humble-to humiliate them. 12 ride sharing can thus express hierarchized and asymmetrical forms of social recognition. similarly, a woman named joana, a squatter at nossa senhora, recalled that before her family secured land of their own, she used to steal bananas and other fruits from neighboring plantations, just to feed her family. on one occasion, she was caught by a plantation manager just as she was cutting down a banana tree. rather than punishing her, the plantation manager simply stated: "just make sure it [the banana tree] doesn't fall on cacao trees." the manager appropriated and transformed her act of theft into an act that expressed his magnanimity and generosity, leaving her humiliated and feeling the "greatest shame" (maior vergonha), as she recalled the episode. thus, the fact that ulisses and his companions had to hide from passing cars, for fear of impending violence, and that local landowners refused them social recognition or other traditional forms of exchange, as honório explained, indicates that the clientelistic sharing economy, at least as it was known formerly, was irrevocably transformed by these land occupations. the former exchange of clientelist favors-that replicated the asymmetrical distribution of material goods and social recognition-burst into relations of increasing enmity, hostility, and occasional violence. as the squatters established themselves as a durable presence on the social landscape, however, new and unexpected sharing and other exchange relations began to emerge, as former parties to patron-client relations faced each other on a more equal footing. following the land occupations that culminated in the late 1990s, new sharing economies emerged among families in local squatter and land reform communities. when the tumult of the initial occupations began to calm, and the squatters divided and distributed equal shares of land to each family (devore 2015:1215-1216), they continued the work of reconstructing their social world. some of these efforts included work to transform forests into agroforests (devore 2017b), the construction of new homes, as well as work on new infrastructure to distribute goods and services such as water and electricity (devore 2017c). these diverse labors occasioned a manifold sharing economy, where people share labor, time, and various other resources that were part of wider processes of social reconstruction. the processes of converting forest into agroforest, in particular, brought intensified demand for seeds, seedlings, cuttings, and other plant materials. the trees and other plants cultivated in these agroforests included a broad range of cash and subsistence crops, such as rubber, cacao, cupuaçu, guaraná, graviola, clove, black pepper, bananas, manioc, and numerous garden crops-and even native tree species (see devore et al. 2019) . demand for these various trees 12 i learned this the hard way sometime in 2003 or 2004 while walking down a country road, when a white man driving a large truck stopped and offered me a ride to my destination. i had never met him before, and had no idea who he was. sometime later, i encountered him again in the town square. although i remembered his face, i could not recall where we had previously met. the man appeared offended and reminded me that he had given me a ride several months prior. later, i realized that he was not offended by the fact that i had forgotten the specific context within which we had met, but rather that i did not remember him, who he was, and what he represented to local society. i later learned that he was a member of one of the region's political elite families. by forgetting who he was, i had failed to honor him. and other plants gave rise to a seed-and plant-sharing economy, as different botanical resources changed hands through tiny gestures, often with few formalities, among families, friends, neighbors, and even strangers. this sharing economy can be seen in different stages of the long-term projects to cultivate agroforests. people clearing new roças from patches of forest might share excess cellulose (e.g., firewood) with neighbors, or trade good pieces of timber for finished wood products (e.g., doors, windows) with which they might outfit their new houses. cultivating newly opened roças required seeds and seedlings, and eventually plant cuttings for grafting material. over time, plant materials that were secured by various means, including sharing, would later become sources of seeds, seedlings, and cuttings that could be shared more widely. for example, manioc is cultivated from cuttings derived from the stems of harvested manioc plants. these cuttings, or mandibas as they are called, grow into new manioc plants when inserted into the ground (see fig. 2 ). when harvested, the discarded stems of mature manioc plants are a source of more mandibas that can be shared with yet others who are preparing to cultivate new manioc gardens of their own. special and rare varieties of bananas are sought after with interest, with banana rhizomes being shared and sometimes traded like collectibles (see fig. 3 ). these bananas provide shade for young cacao trees, the seeds for which may come from cacao pods that were shared among friends and neighbors seeking to establish tree nurseries of their own (see fig. 4 ). rubber tree seeds can be collected freely along roadsides-a de facto commons-where rubber trees deposit large quantities of seeds at certain times of the year. cuttings from rose bushes, orchids growing on the sides of trees, and various herbal and medicinal plants are shared and transplanted across farms and among households. seeds and cuttings from various fruits trees, or cuttings from the branches of improved varieties of cacao or rubber, are shared among households and grafted into young trees already growing in their gardens and orchards (see fig. 5 ). novel tree and fruits, such as rambutans and mangosteens, circulate as people's palates adjust to new flavors, and new niche markets grow. the democratization property in land, and the generalized distribution of plants, also led to novel expressions of land sharing and sharecropping. one particular squatter at nossa senhora named galeno bought a flatbed truck and began buying banana harvests from neighboring squatter families, which he then resold for a profit at a regional market in a town called wenceslau guimarães. to foster these market activities, galeno readily provided labor from his own family, and banana rhizomes from his own farm, to help other squatter families establish banana groves that would eventually provide shade for young cacao and rubber trees of their own. as a local buyer, galeno had a clear interest in offering plants and labor to other squatters, as he would later buy their banana harvests. but he provided these resources free of any cost, articulating an ethos of solidarity by emphasizing the importance of "giving" (dar) and "donating" (doar) such resources to people of humble origins, like himself. by contrast, he emphasized that the "rich" could and should pay for such things. unlike other forms of sharecropping described in previous sections, however, galeno helped these local families establish cacao and rubber groves of their own-effectively helping them to creating durable (re)productive capital and capacities of their own. the squatter families with whom galeno did business began as havenots, in possession of land that they barely had the resources to cultivate by themselves. these families ended with land cultivated in productive and durable agroforests. thus, although he had a clear personal interest in sharing labor, plants, and other resources with neighboring squatters, galeno also helped to close the resource gap between his own and other families, rather than reaffirming the difference that characterized their starting points, as haves and have-nots. this form of sharing was transformative, rather than replicating the initial difference between galeno and other squatters. another significant development arose in the previously asymmetrical exchanges between plantation owners and former plantation laborers who became squatters. by contrast to the enmity and violence that initially characterized relations between landowners and squatters following the land occupations, a sharing economy has gradually emerged over the years between these formerly opposed parties. not only have "good days" and ride-sharing (caronas) returned to squatters, many of whom continue to travel by foot, but now some plantation managers even offer tractors, trailers, and other plantation vehicles to help squatters achieve larger purposes. on one occasion, for example, a plantation manager helped one family move their personal belongings and furniture from a former dwelling in a community called pequi to a new house that the family built on their farm (see fig. 6 ). on another occasion, a plantation manager helped another family transport large steel plates to their farm, which were crucial bits of infrastructure used to build drying ovens for cacao and other products. the kinds of ride-sharing offered by plantation managers not only helped squatter families get from point a to point b but also participated directly in squatters' efforts to transform the material conditions of their lives. through cultivation processes, moreover, further exchanges have appeared between squatter communities and their neighboring plantations. some plantation managers freely offer plant cuttings and grafting material from improved varieties of cacao and rubber, which have been bred for increased productivity and disease resistance. like the rare and special banana varieties, squatters collect diverse clone material that they graft into the rubber and cacao trees growing on their own roças. although squatters may have materially less to share in return, the sharing economy goes both ways. squatters may offer surplus from their fruit harvests with plantation workers and managers alike. some may collaborate on shared infrastructure projects, such as road maintenance, or share excess firewood from their recently cleared roças. some young (environmentally conscious) squatters, more recently, have supported efforts by local plantations to plant native tree species on their landholdings, gathering and delivering tree seeds that grow on and around their own farms. figure 7 summarizes 50 acts of sharing through acts of sharing and exchanging plants, labor, and various other resources, local squatter families achieve several outcomes. first, as their plants grow and mature, they further generalize the availability of plant materials that can be objects of future exchanges with and distributions to other people. second, unlike cultivating impermanent annual crops, shared seeds, seedlings, and cuttings eventually grow into durable trees and perennials that substantially transform local communities' capacities for social and material (re)production. third, by cultivating a diverse and living assortment of trees and other perennials-all "root goods"local squatter families further consummate and secure their claims to land. like an inverse image of woodburn's egalitarian sharing that dissolved property, people in these squatter communities leveled social hierarchies, but they did so by democratizing property for all. by contrast with those forms of sharing that merely replicated and reaffirmed the unequal status of participants at the outset, the sharing of long-lived plants transformed both social and biophysical landscapes in ways such that people emerged-together with their trees-as reconstructed subjects. although the redistribution of land that occurred in the 1990s was powerful and meaningful for hundreds of local families, it was also limited, as it did not end problems of landlessness from sharecropping to equal shares: transforming the sharing economy in... nonetheless, the redistribution and democratization of meaningful control of land, rather than mere access to land, also occasioned novel acts and expressions of sharing. the basis for the reconstructed sharing economy described above-and what makes it qualitatively different from preceding forms of sharing and sharecropping in the region-is that the parties to these exchanges have more closely approximated what nancy fraser (2001) calls "participatory parity." as i have suggested elsewhere, in an analysis of distributive struggles that occurred internal to several of the region's mst settlements, the achievement of participatory parity required the creation of "conditions under which no one party had the power to illegitimately disenfranchise the other, and each could support the other in shared work and political struggle" (devore 2015:1219). these conditions, as fraser (2001:36) suggests, require, in part, equitable distributions of the "objective" (i.e., material) conditions that make such parity possible. in southern bahia, significant steps toward the achievement of participatory parity occurred through increased democratization of land ownership. as such conditions were established, or at least approximated, new and less coercive forms of social interaction emerged, including new and more egalitarian expressions of sharing. these forms of sharing were also transformative, as they helped to reconstruct and extinguish the asymmetrical form of society out of which they arose. as people shared and exchanged root goods-especially incipient trees in the forms of seeds, seedlings, and cuttings-these temporally durable plants helped consolidate the claims that landless rural proletarians made to land for themselves, as they emerged as a reconstituted peasantry. in short, the reconstructed sharing economy that arose from their land occupations propelled the ongoing reconstruction and transformation of society. but the distinction i proposed above between transformative and replicative sharing cannot be drawn so hard and fast. while replicative forms of sharing tend to reproduce the form of society from which they arise, they may also plant seeds for a new society. indeed, the peasant breach phenomenon, in particular, witnessed unintended social consequences of shared land through nineteenth century provision grounds, which militated against enslaved people's legal status and institutional roles as mere property objects. in this sense, as marx learned from hegel, even routinized, apparently replicative forms of sharing may bear the seeds of their own destruction. what properly belongs to me: kant on giving to beggars revolutionary politics and locke's two treatises of government the slave economy of nineteenth century bahia: export agriculture and local market in the reconcavo a bit of land, which they call roça': slave provision grounds in the bahian recôncavo unequal democracy: the political economy of the new gilded age sharing nicely: on shareable goods and the emergence of sharing as a modality of economic production the slaves' economy: independent production by slaves in the americas a spirit of trust: a reading of hegel's phenomenology agricultura, escravidão e capitalismo the peasant breach in the slave system: new developments in brazil slaves, freedmen and the politics of freedom in brazil: the experience of blacks in the city of rio sharing and neoliberal discourse: the economic function of sharing in the digital ondemand economy what hegel's master/slave dialectic really means regions of refuge cultivating hope: struggles for land, equality, and recognition in the cacao lands of southern bahia the landless invading the landless: participation, coercion, and agrarian social movements in the cacao lands of southern bahia reflections on crisis, land, and resilience in brazil's politics of distribution odebrecht's original sins: another case for reparations trees and springs as social property: a perspective on degrowth and redistributive democracy from a brazilian squatter community theorizing the contemporary, fieldsights scattered limbs: capitalists, kin, and primitive accumulation in brazil's cacao lands, 1950s-1970s afterword: from affirmative to transformative distributive politics conserver la nature humaine et non humaine. un curieux cas de conservation conviviale au brésil kant's socialism: a philosophical reconstruction give a man a fish: reflections on the new politics of distribution explaining the biogeography of the medium and large mammals in a human-dominated landscape in the atlantic forest of bahia, brazil: evidence for the role of agroforestry systems as wildlife habitat late soviet ecology and the planetary crisis crossroads of freedom: slaves and freed people in bahia, brazil from redistribution to recognition? dilemmas of justice in a 'postsocialist' age social justice in the age of identity politics: redistribution, recognition, and participation roll, jordan, roll: the world the slaves made from sharecropping to equal shares: transforming the sharing economy in phenomenology of spirit commons. in degrowth: a vocabulary for a new era metaphysical elements of justice: part one of the metaphysics of morals, trans metaphysical elements of justice: part one of the metaphysics of morals economic cycles in brazil: the persistence of a total-culture pattern. cacao and other cases the works of john locke in nine volumes the world cacao made: society, politics, and history in southern bahia, brazil the geology of mankind? a critique of the anthropocene narrative the sharing economy: a pathway to sustainability or a nightmarish form of neoliberal capitalism? capital: a critique of political economy the russian peasantry, 1600-1930: the world the peasants made the capitalocene, part i: on the nature and origins of our ecological crisis the capitalocene, part ii: accumulation by appropriation and the centrality of unpaid work/energy neoliberal eclipse: donald trump, corporate monopolism, and the changing face of work carteira assinada: 'tradicionalismo do desespero why the gilded age the end of the peasantry: the rural labor movement in northeast brazil primeira ocorrência de vassoura-debruxa na principal região produtora de cacau do brasil the role of work within the processes of recognition in hegel's idealism resistance and accommodation in eighteenth-century brazil: the slaves' view of slavery slaves, peasants, and rebels: reconsidering brazilian slavery the art of not being governed: an anarchist history of upland southeast asia late marx and the russian road: marx and 'the peripheries of capitalism a função ideológica da brecha camponesa tratado descriptivo do brasil em 1587 begging. in the egalitarian conscience: essays in honour of g custom, law and common right plano de ação econômica para o estado da bahia the right to private property governing tsarist russia african oil palms, colonial socioecological transformation and the making of an afro-brazilian landscape in bahia anthropology and the economy of sharing philosophical investigations egalitarian societies publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations key: cord-011669-hkkpw2bl authors: rodríguez-sánchez, diego noé; pinto, giovana boff araujo; thomé, edval fernando; machado, vânia maria de vasconcelos; amorim, rogério martins title: lissencephaly in shih tzu dogs date: 2020-06-20 journal: acta vet scand doi: 10.1186/s13028-020-00528-0 sha: doc_id: 11669 cord_uid: hkkpw2bl background: lissencephaly is a brain malformation characterized by smooth and thickened cerebral surface, which may result in structural epilepsy. lissencephaly is not common in veterinary medicine. here, we characterize the first cases of lissencephaly in four shih tzu dogs, including clinical presentations and findings of magnetic resonance imaging of lissencephaly and several concomitant brain malformations. case presentation: early-onset acute signs of forebrain abnormalities were observed in all dogs, which were mainly cluster seizures and behavioral alterations. based on neurological examination, the findings were consistent with symmetrical and bilateral forebrain lesions. metabolic disorders and inflammatory diseases were excluded. magnetic resonance imaging for three dogs showed diffuse neocortical agyria and thickened gray matter while one dog had mixed agyria and pachygyria. other features, such as internal hydrocephalus, supracollicular fluid accumulation, and corpus callosum hypoplasia, were detected concomitantly. antiepileptic drugs effectively controlled cluster seizures, however, sporadic isolated seizures and signs of forebrain abnormalities, such as behavioral alterations, central blindness, and strabismus persisted. conclusions: lissencephaly should be considered an important differential diagnosis in shih tzu dogs presenting with early-onset signs of forebrain abnormalities, including cluster seizures and behavioral alterations. magnetic resonance imaging was appropriate for ante-mortem diagnosis of lissencephaly and associated cerebral anomalies. lissencephaly in mammals occurs due to the failure of neuroblasts to migrate to the cerebral cortex, during development [1, 2] . it is characterized by smooth cortical appearance and by the absence of surface folds (agyria) or abnormally broad folds (pachygyria). histopathology demonstrates thickening of the cerebral cortex, altered gray-to-white matter ratio and replacement of a normal 6-layered cortex with a 4-layered disorganized cortex [2, 3] . two types of lissencephaly can be distinguished in humans: classical lissencephaly (or type i), characterized by thickened brain surface with agyria or pachygyria that results from neuronal migration arrest [4, 5] and cobblestone lissencephaly (or type ii), characterized by thin and nodular brain surface, resulting from glial and neuronal overmigration [4, 5] . muscular dystrophy, ocular alterations, obstructive hydrocephalus, and malformation of the brainstem and cerebellum are often associated with cobblestone lissencephaly [4] [5] [6] . lissencephaly has been described in lhasa apso [7, 8] , pekingese [9] , australian kelpie [10] , wire-haired fox terrier [11] , irish setter [11] , and mixed-breed dogs [12] . in humans, lissencephaly is associated with gene mutations related to brain development or cerebral metabolism [1, 5, 13] . in addition, nongenetic causes, such as intrauterine viral infections, vascular events (hypoxia or hypoperfusion), and maternal metabolic disorders that interrupt cortical formation, have been described [2, 3, 13] . the neurological signs in dogs commonly begin with an early-onset of seizures and behavioral alterations, leading to disability [7, 8, 10] . clinical findings and magnetic resonance imaging (mri) features of lissencephaly in shih tzu dogs have not been reported previously, and reports of concomitant brain malformations are scarce. four apparently unrelated shih tzu dogs were presented with lissencephaly between 2011 and 2018 at the veterinary neurology service of são paulo state university (unesp), brazil. details regarding clinical features, neurolocalization, ancillary diagnostics and antiepileptic treatment are shown in table 1 . mri was performed using a 0.25 tesla scanner (vet-mr grande, esaote, italy) in all dogs to obtain t1-weighted, t2-weighted, fluid-attenuated inversion recovery (flair) and postcontrast t1 sequences. in addition, gradient echo (gre) sequences were obtained in three dogs, and hybrid contrast enhancement (3d hyce) sequences were obtained in two dogs. all mris were evaluated and interpreted by two researchers (ra and vm). a summary of the mri findings, equipment, positioning, sequences, imaging parameters, and the contrast medium are detailed in additional file 1. the first case was an 8-month-old spayed female referred in 2011 due to seizures of suspected idiopathic origin that were poorly controlled with phenobarbital (gardenal ® , 2.5 mg/kg, orally q12h; safoni, brazil). the dog was evaluated by the referring veterinarian 2 months after the onset of tonic-clonic seizures, which had progressed over the last 2 weeks to 2-3 seizures per week. in our service, the owner reported that the dog experienced cluster seizures that occurred over 48 h and were treated with diazepam and thiopental. on presentation, neurological examination was performed 1 week after cluster seizures and was unremarkable. based on a history of seizures, the lesion was localized to the forebrain. physical examination findings, biochemical profile, and complete blood count (cbc) were normal; polymerase chain reaction (pcr) for canine distemper virus in urine and indirect immunofluorescent antibody tests (ifat) for antibodies against toxoplasma gondii and neospora caninum were negative. mri showed mixed parieto-occipital agyria and pachygyria of the frontal and parietal lobes (fig. 1 ). temporal and occipital regions lacked gyri and sulci. mri diagnosis indicated lissencephaly and supracollicular fluid accumulation (sfa) (fig. 1) . treatment with phenobarbital (gardenal ® , 3 mg/kg, orally q12h; safoni, brazil) and levetiracetam as an adjunct (keppra ® , 20 mg/kg, orally q8h; ucb biopharma, brazil) effectively controlled cluster seizures after presentation. levetiracetam was discontinued after 4 weeks. the neurological signs were nonprogressive and this dog experienced only isolated episodes (interictal period of 2-3 months) over a period of 24 months after diagnosis of lissencephaly (> 50% reduction in the frequency of seizures). it was not possible to obtain information regarding survival for this dog. the second case involved a 43-month-old castrated male which was referred in 2014 due to the occurrence of cluster seizures. the dog was diagnosed by the referring veterinarian with presumed idiopathic epilepsy at 24 months of age and treatment with phenobarbital was then initiated (gardenal ® , 2.5 mg/kg, orally q12h; safoni, brazil). during the first 16 months after diagnosis of presumed idiopathic epilepsy and the onset of treatment, the dog experienced both isolated seizures and cluster seizures, with an interictal period less than 30 days. relatively low levels of phenobarbital (< 25 µg/ ml: therapeutic window 25-35 µg/ml) were detected in serum; therefore, the dose of phenobarbital was gradually increased (gardenal ® , 4 mg/kg, orally q12h; safoni, brazil). however, despite the increase in serum phenobarbital concentration (35 µg/ml), the dog continued to have repeated tonic-clonic seizures. therefore, potassium bromide (kbr) (30 mg/kg orally, q24h) was also prescribed 1 month before referral to unesp. on presentation in our service, in addition to cluster seizures the owner reported behavioral changes between seizures, such as difficulties in learning basic commands, changes in sleep cycle and compulsive pacing. aggression was noted in our service during manipulation for physical examination. during anamnesis, the owner reported polyuria, polydipsia and polyphagia. biochemical profile showed increased levels of alkaline phosphatase (216: reference interval 20-156 u/l). these alterations were presumed to be associated with phenobarbital treatment. neurological examination revealed no abnormalities except for the presence of bilateral central blindness and bilateral ventromedial strabismus during cranial nerve examination. physical and ophthalmological examinations were normal. the anatomical neurolocalization was compatible with a forebrain lesion. pcr in urine for canine distemper virus and ifat in the serum for t. gondii and n. caninum were negative. mri showed absence of sulci and gyri with superficial undulations in the frontal and temporal lobes. the main gyri, including the marginal, ectomarginal, suprasylvian, and ectosylvian gyri, were absent. a rudimentary lateral rhinal sulcus was present, while the cingulate gyrus was not apparent. the internal capsule was abnormally small (fig. 1) . a diagnosis of lissencephaly, internal this dog remained stable and neurological signs were nonprogressive for 36 months after diagnosis of lissencephaly (interictal interval of 3-4 months with > 50% reduction in the frequency of seizures) using combined polytherapy involving both phenobarbital (gardenal ® , 4 mg/kg, orally q12h; safoni, brazil) and kbr (30 mg/ kg, orally, q24h). levetiracetam (keppra ® , 20 mg/kg, orally q8h for 4-6 weeks, ucb biopharma, brazil) was initially included as an adjunct treatment modality. no more cluster seizures were reported after presentation. a carbonic anhydrase inhibitor (acetazolamide, diamox ® , 10 mg/kg, orally q8h, genom, brazil) and a proton-pump inhibitor (omeprazole, gaviz ® , 10 mg/dog, orally q24h, agener, brazil) were used for supportive treatment of hydrocephalus. however, the difficulties in learning basic commands, changes in sleep cycle, compulsive pacing, strabismus and aggression were persistent despite treatment. phone conversation with the owner revealed that the dog was alive 6 years after diagnosis. the third case involved an 18-month-old intact male which was referred in 2014 due to the occurrence of cluster seizures starting 12 days prior to referral. the dog was previously treated with phenobarbital (gardenal ® , 6 mg/kg, orally q12h; safoni, brazil); however, due to poor response to treatment, adjunctive therapy with kbr (40 mg/kg, orally, q24h) was initiated. on presentation, anamnesis revealed that 6 months prior to referral, the dog had experienced over 14 isolated seizures within 45 days and subsequent episodes monthly. at evaluation, the dog experienced two tonic-clonic seizures, and emergency treatment was provided using diazepam (1 mg/kg, per rectum and repeated iv bolus 3x). during the 48-h postictal re-evaluation, neurological examination revealed central blindness, and the owner reported that the dog demonstrated abnormal vocalizations. in addition, aggressiveness during the interictal period was noted, mainly during dog handling. anatomical neurolocalization was consistent with a forebrain lesion. physical and ophthalmological examination was unremarkable. laboratory data, including pcr in urine for canine distemper virus and ifat in the serum for t. gondii and n. caninum were negative. mri of the third dog showed presence of some sulci in the temporal lobe, including the caudal sylvian gyri and lateral rhinal sulci. however, the main gyri, including the marginal, ectomarginal, suprasylvian gyri, and suprasylvian sulcus (division between the parietal and temporal lobe), were absent (fig. 2) . the internal capsule was abnormally small. diagnosis was consistent with lissencephaly, asymmetrical internal hydrocephalus, and corpus callosum hypoplasia. this dog showed progressive reduction in isolated seizures throughout the year following diagnosis (> 50% reduction in seizure frequency) with an interictal interval of 2 months, maintaining combined polytherapy involving phenobarbital (gardenal ® , 6 mg/kg, orally q12h; safoni, brazil) and kbr (30 mg/kg, orally, q24h). serum concentration of phenobarbital was not tested due to financial constraints. no more cluster seizures were observed with combined polytherapy. a carbonic anhydrase inhibitor (acetazolamide, diamox ® , 10 mg/kg, orally q8h, genom, brazil) and a proton-pump inhibitor (omeprazole, gaviz ® , 10 mg/dog, orally q24h, agener, brazil) were used for supportive treatment of hydrocephalus. behavioral changes and central blindness persisted despite treatment. overall survival was 6 years after diagnosis, confirmed by the owners after our phone call. the fourth case was an 18-month-old spayed female which was referred with seizures in 2018. the referring veterinarian suspected meningoencephalitis of unknown etiology and reported poor control of seizures with phenobarbital (gardenal ® , 2 mg/kg, orally q12h; safoni, brazil). prednisolone treatment (predsim ® , 0.5 mg/kg, orally q12h; medley, brazil) was added empirically 1 week prior to referral by the referring veterinarian. in our service, the owner reported the first isolated tonic-clonic seizure when the dog was 9 months old. after the interictal period of 9 months, the owner reported that these seizures began again 3 weeks prior to examination. over the 3-week period before examination, during the interictal periods, subtle behavioral changes such as aggressiveness (mainly after handling), compulsive pacing, abnormal vocalizations, and licking at things were observed. the dog presented with cluster seizures in our service and was treated with diazepam. after stabilization, the postictal state in the following 24 h was characterized by ataxia, paresis, and behavioral signs. upon neurological examination after postictal stage, consciousness, posture, gait, and postural reactions were normal. cranial nerve examination showed bilateral central blindness and bilateral ventromedial strabismus. the findings were consistent with a forebrain lesion. physical and ophthalmological examination findings, biochemical serum profile and cbc test results were unremarkable. thorax radiography and abdominal ultrasound did not show alterations. pcr in urine for canine distemper virus and , h) in the third and fourth cases. mri of the third dog showed a few sulci in the temporal lobe, including the caudal sylvian gyri and lateral rhinal sulci (arrow). the main gyri (including the marginal, ectomarginal and suprasylvian) and the suprasylvian sulcus were absent. the internal capsule was abnormally small, and internal hydrocephalus was visualized (a-d). mri of the fourth dog showed generalized agyria with an absence of sulci and thickened gray matter with smooth appearance (arrow) (e, f). rhinal sulci in the temporal lobe were not apparent and cingulate gyrus was absent (arrowhead). internal hydrocephalus and supracollicular fluid accumulation associated with dorsocaudal outpocketing of the third ventricle (type sfa-iii) were observed (g, h) ifat in the serum for t. gondii and n. caninum were negative. mri showed generalized absence of sulci and gyri and thickened gray matter. the main sulci and gyri, including the marginal, ectomarginal, suprasylvian, ectosylvian, and lateral rhinal sulci, were absent. the cingulate gyrus was not recognizable, and the subcortical internal capsule was abnormally small (fig. 2) . the diagnosis was consistent with lissencephaly with sfa, internal hydrocephalus and corpus callosum hypoplasia. prednisolone was then discontinued due to lack of indication. clinical presentation and mri did not support a diagnosis of meningoencephalitis. after dose readjustment with phenobarbital (gardenal ® , 2.7 mg/kg, orally q12h; safoni, brazil) and levetiracetam as an adjunct (keppra ® , 20 mg/ kg, orally q8h for 4 weeks; ucb biopharma, brazil), seizure frequency was reduced for the first 3 months (> 50% frequency reduction of seizures). adjunct treatment with levetiracetam was discontinued after approximately 4 weeks. at the 12-month follow-up examination, seizure reduction with an interictal interval over 2-3 months was noted and no more cluster seizures were observed. however, the behavioral changes, blindness and strabismus observed were persistent despite treatment. a phone conversation with the owners revealed that the dog was alive at the time of writing this report 2 years after diagnosis. malformations of cortical development have rarely been reported in dogs, but epileptic seizures seem to be a frequent clinical sign in affected dogs [7, 9, 10] . lissencephaly represents an uncommon disorder of the cortical gyration in dogs [7, 9, 10] . lissencephaly without concurrent intracranial malformations was described in lhasa apso dogs, in an australian kelpie dog and in a small mixed-breed dog [7, 10, 12] . this report is the first on lissencephaly in shih tzu dogs with other concurrent intracranial malformations and the first report providing a detailed neuroanatomical description of lissencephaly identified on mri. in humans, malformations of cortical development can lead to lissencephaly type i, characterized by pachygyria or agyria with thickened and smooth brain surface [4, 5] . apart from lissencephaly, cortical development disorders that may cause epilepsy as subcortical band heterotopia, polymicrogyria, and cobblestone malformations have been described [1, 2] . such disorders are rarely reported in dogs [14] . four shih tzu dogs without any known close relationship, were referred because of epileptic seizures. the dogs were not selected among breeds. the onset of seizures was at the age of 6, 9, 12 and 24 months. previous studies have reported the onset of seizures in dogs between the age of approximately 12 months and 5 years in two lhasa apso [7, 8] , one pekingese [9] , one australian kelpie [10] , and one mixed-breed dog [12] . in humans with lissencephaly, approximately 83% of patients experience earlyonset seizures earlier than 7-months-old [15] . neuro-ophthalmological abnormalities have been poorly characterized in dogs with lissencephaly. central blindness was previously reported [7, 9] . we detected central blindness in three out of four dogs. bilateral vision deficits were thought to derive from occipital lobe lesions. bilateral ventromedial strabismus (esotropia) was detected in two out of four dogs. only one other report has described ventromedial strabismus in a dog with lissencephaly, which was associated with an orbital anatomical abnormality or short medial rectum muscle [7] . we assumed that maldevelopment of the primary visual cortex and visual motor control mechanism may lead to esotropia [16] . humans with lissencephaly have visual abnormalities, including no ocular fixation or tracking, poor visual tracking, nystagmus, variable esotropia, oculomotor apraxia, optic nerve and macular hypoplasia/ atrophy, delayed visual maturation, and cortical visual impairment [17] . approximately 67% of human patients with lissencephaly type i have neuro-ophthalmological abnormalities [17] . severe mental retardation may be observed in humans with lissencephaly and is associated with neuronal migration defects in spatial learning areas [3, 5, 18] . motor disability as early hypotonia, spastic tetraplegia and opisthotonos is observed in human cases of lissencephaly due to defects in motor areas [3, 5] . humans with lissencephaly often die before adulthood [1, 6, 17] . in our study, early onset of several behavioral changes was detected in three dogs between 6 and 24 months old. alterations in locomotor behavior (pacing and changes in sleep pattern), aggressiveness (irritability to manipulation) and vocalization in addition to seizures were observed. previous studies observed late-onset behavioral changes in dogs with lissencephaly over 12-months-old [7] [8] [9] [10] 12] , aggressiveness being frequently reported [7, 9, 10] . the different clinical pictures between human and canine lissencephaly could be explained by the fact that the cerebral cortex is less essential in dogs than in humans for motor function [11] . in dogs, motor function may be maintained despite frontoparietal lobe (motor area) and pyramidal system lesions. however, cognitive and learning abilities may be affected [11] . magnetic resonance imaging in dogs with lissencephaly showed thickened cortical gray matter with smooth appearance, an abnormally small internal capsule, and absence of the major gyri and sulci when compared with healthy shih tzu dogs (additional file 2). previous studies did not report detailed neuroanatomical examinations of cortical gyri and sulci in dogs with lissencephaly [7, 9, 10] . in addition, mri was informative for correct ante-mortem diagnosis of multiple congenital anomalies, determination of cerebral morphology, and the degree of lissencephaly in shih tzu dogs. lissencephaly is graded in humans using a 6-point grading system based on the severity and anterior-posterior brain gradient of the abnormalities. grade 1 represents severe lissencephaly with complete agyria, while grade 6 represents mild subcortical band heterotopia [3, 5] . grades 1a to 6a are more severe posteriorly and 1b to 6b anteriorly [3, 5] . using these criteria, the second (fig. 1e) , third (fig. 2a) and fourth (fig. 2e) cases presented here were classified as grade 2a with diffuse agyria and few shallow undulations in the frontal and temporal lobes. the first dog was classified as grade 3a due to mixed parieto-occipital agyria and frontal pachygyria (fig. 1a) . previous studies have reported lissencephaly grade 2a [9] and 2b [10] in dogs. in our study, behavioral alterations and central blindness were noted in dogs with more severe lissencephaly grade, indicating a possible correlation between mri severity and clinical signs. the grade of lissencephaly was not related to the severity of the clinical signs in previous studies [9, 10] . two forms of lissencephaly have been described in humans: classic lissencephaly (or type i), characterized by abnormal thick cortical layers (four layered, with a cell-sparse zone), agyria or pachygyria without malformation of the brainstem and cerebellum [2] . mutations in cytoskeletal genes, such as the platelet activating factor acetylhydrolase 1b regulatory subunit 1, doublecortin, and tubulin a1a genes [1, 2, 5] , can lead to lissencephaly in humans and mice [1, 5] . cobblestone lissencephaly (type ii) is characterized by multiple shallow furrows, a thin cerebral mantle and malformation of the brainstem and the cerebellum [2, 5] . in dogs, genetic mutations for lissencephaly have not yet been described [7, 11] . in our study, muscular and ocular disorders were not observed and mri did not showed nodular brain surface and brainstem or cerebellum malformations associated to cobblestone lissencephaly [4] [5] [6] . therefore, our dogs likely have lissencephaly analogous to type i human lissencephaly [2, 5, 19] . lissencephaly is overrepresented in the lhasa apso dogs and was also reported in the genetically related pekingese breed [7, 9] . considering the genetic relation among lhasa apso, pekingese and shih tzu breeds [20] , it is possible that lissencephaly may be a genetic disease in dogs. hydrocephalus and sfa are intracranial malformations most often reported in young and toy breed dogs [21] [22] [23] . enlarged ventricles (a condition known as ventriculomegaly) comprise a common finding in adult brachycephalic dogs [21, 23] . dogs with only ventriculomegaly do not have increased intraventricular pressure and are considered to be asymptomatic [21, 23] in our study, internal hydrocephalus was confirmed based on specific mri features that indicated increased intraventricular pressure in three dogs [21] . hydrocephalus with concomitant lissencephaly has not been reported in dogs. in dogs, lissencephaly has been diagnosed together with ventriculomegaly rather that with hydrocephalus [7, 10, 12] . in a human study, ventriculomegaly has been observed in 73.7% of patients with lissencephaly type i [15] . supracollicular fluid accumulation without concomitant lissencephaly has been reported in male brachycephalic dogs, and the shih tzu dog breed was most often reported [22] . in dogs, most sfas are associated with dorsocaudal outpocketing of the third ventricle (sfa-iii) [24] . an expansion of both the third ventricle and the quadrigeminal cistern is another type of sfa (sfa iii-qc) [24] . a few cases present with enlargement of the sole quadrigeminal cistern (sfa-qc) [24] . previously, it was hypothesized that type sfa-iii in predisposed breeds can be part of hydrocephalus rather than an anomaly itself [24] . in our study, the first dog presented with sfa-qc and type sfa-iii was detected in the second and fourth dogs. although sfa can be related to the presence of neurological signs in dogs with lissencephaly, the clinical significance of sfa is variable and sfa may be incidental in dogs with other intracranial diseases [22] . there is no reported genetic relationship between sfa and lissencephaly in neither dogs nor humans. in humans, supracollicular fluid accumulation is associated with a defect in leptomeninges development [19] . corpus callosum abnormalities have been sporadically reported and are still poorly understood in dogs, typically being an isolated abnormality or associated with holoprosencephaly and inborn errors of metabolism. the most frequent clinical signs described are hypodipsia/ adipsia, tremors, and seizures [25] . we observed concurrent corpus callosum hypoplasia in the second, third, and fourth dogs, which is not commonly reported in dogs with lissencephaly [11] . epileptic seizures may be related to corpus callosum hypoplasia. in humans, corpus callosum abnormalities are associated with classic lissencephaly (type i), cobblestone lissencephaly (type ii) and polymicrogyria [2, 15] . the antiepileptic drugs used resulted in good control of cluster seizures with mild adverse effects in the long-term follow-up (12-36 months). seizures were persistent, although, compared to pretreatment, a reduction in the frequency (> 50% or more) and severity of seizures as well as cessation of cluster seizures was observed. other signs of forebrain abnormalities, such as behavioral alterations, central blindness, and bilateral strabismus were persistent. several medications, including carbonic anhydrase inhibitor acetazolamide and proton-pump inhibitor omeprazole, with the goal of decreasing cerebrospinal fluid production, have been proposed as medical management in dogs with hydrocephalus [23, 26, 27] . experimental studies in healthy dogs and rabbits reported that cerebrospinal fluid production was reduced after acetazolamide and omeprazole treatment, respectively [26, 28] . due to hydrocephalus, the second and third dogs were medically treated with acetazolamide and omeprazole. nevertheless, aggressiveness, changes in sleep cycle, compulsive pacing, central blindness, and strabismus were persistent during the follow-up period despite treatment with acetazolamide and omeprazole. one previous report has described no significant effects on recovery of the neurological signs or ventricular volume reduction after treatment with acetazolamide in dogs with hydrocephalus [29] . furthermore, chronic oral omeprazole therapy in healthy dogs did not affect cerebrospinal fluid production [30] . the major limitation of this study was the lack of histopathological evaluation, which was not possible because dogs were not euthanized during the follow-up period. although transcranial ultrasonography or computed tomography may aid in diagnosis, these methods are not precise [9, 10] . in our study, the use of low-field mri provided a good resolution for ante-mortem diagnosis of lissencephaly in all dogs. variations in signal intensity, identification of abnormal cortical layers and depth of cortical sulci were observed. all anatomical structures of the cerebral cortex were identified (additional file 2). in agreement, previous studies performed diagnosis in dogs using mri fields between 0.4-and 1.5-tesla [7, 9, 10] . mri is the modality of choice for lissencephaly diagnosis and for the differentiation of other neuronal migration disorders, showing a correlation with histopathological features in dogs and humans [1, 2, 7] . lissencephaly should be considered an important differential diagnosis in shih tzu dogs presenting predominantly with early-onset signs of forebrain abnormalities, including tonic-clonic seizures, behavioral alterations, central blindness, and bilateral ventromedial strabismus. low-field mri may be a useful diagnostic tool to detect cases of lissencephaly. hydrocephalus, sfa, and corpus callosum hypoplasia comorbidities could also be associated with lissencephaly in shih tzu dogs. genetic malformations of cortical development a developmental and genetic classification for malformations of cortical development: update 2012 lissencephaly and other malformations of cortical development: 1995 update genetic basis of brain malformations the genetics of lissencephaly neuropathology of lissencephalies. child's nerv syst magnetic resonance imaging features of lissencephaly in 2 lhasa apsos lissencephaly in two lhasa apso dogs lissencephaly in a pekingese lissencephaly in an adult australian kelpie veterinary neuroanatomy and clinical neurology clinical and mri findings of lissencephaly in a mixed breed dog inborn errors of metabolism leading to neuronal migration defects polymicrogyria in standard poodles lis1-related isolated lissencephaly brain abnormalities in infantile esotropia as predictor for consecutive exotropia ocular findings in lissencephaly wynshaw-boris a. impaired learning and motor behavior in heterozygous pafah1b1 (lis1) mutant mice a developmental and genetic classification for midbrain-hindbrain malformations genetic structure of the purebred domestic dog magnetic resonance imaging signs of high intraventricular pressure-comparison of findings in dogs with clinically relevant internal hydrocephalus and asymptomatic dogs with ventriculomegaly clinical and magnetic resonance imaging characteristics of quadrigeminal cysts in dogs congenital hydrocephalus multidetector computed tomographic and low-field magnetic resonance imaging anatomy of the quadrigeminal cistern and characterization of supracollicular fluid accumulations in dogs corpus callosal abnormalities in dogs inhibition of cerebrospinal fluid formation by omeprazole different effects of omeprazole and sch 28080 on canine cerebrospinal fluid production effect of certain drugs on cerebrospinal fluid production in the dog effect of acetazolamide and subsequent ventriculo-peritoneal shunting on clinical signs and ventricular volumes in dogs with internal hydrocephalus evaluation of the effect of oral omeprazole on canine cerebrospinal fluid production: a pilot study publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations the authors are grateful to heraldo andré catalan rosa for technical support with mri. data have not been published previously. supplementary information accompanies this paper at https ://doi. org/10.1186/s1302 8-020-00528 -0.additional file 1: table s1 . doc. summary of magnetic resonance imaging (mri) findings of lissencephaly and concomitant congenital malformations in shih tzu dogs. details regarding malformation type, mri scan, positioning of the patient, sequence types, imaging parameters and contrast medium are described.additional file 2: figure s1 . doc. brain magnetic resonance imaging (mri) in a healthy shih tzu dog. transverse t1-weighted (a and b) and transverse and sagittal t2-weighted (c and d) imaging. the following structures were identified at the level of the interthalamic adhesion: marginal gyri (a); marginal sulci (b); middle ectomarginal gyri (c); ectomarginal sulci (d); middle suprasylvian gyri (e); middle suprasylvian sulci (f ); middle ectosylvian gyri (g); caudal ectosylvian sulci (h); caudal sylvian gyri (i); pseudosylvian fissure (j); lateral rhinal sulci (k); splenial sulci (l); cingulate gyri (m) and corpus callosum (o) (a). the following structures were identified at the level of the mesencephalic aqueduct: marginal gyri (a); marginal sulci (b); middle ectomarginal gyri (c); ectomarginal sulci (d); caudal suprasylvian gyri (e); caudal suprasylvian sulci (f ); ectosylvian gyri (g); lateral rhinal sulci (h); parahippocampal gyri (i) and caudal composite gyri (j) (b). in transverse and sagittal t2-weighted images, all anatomical structures were normal, including the lateral ventricles, quadrigeminal cistern and corpus callosum (c and d). authors' contributions dnrs and rma conceived and designed the study. dnrs, gbap, eft and vmm performed the diagnostic work-up, clinical assessment, and provided professional discussion regarding the cases. rma and vmm evaluated and interpreted magnetic resonance imaging. dnrs and gbap wrote the manuscript. rma critically revised the manuscript. all authors read and approved the final manuscript. not applicable. mri equipment was acquired through funding (procedure number 2009/54028-8) provided by the são paulo research foundation (fapesp). the datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. this study was not submitted for ethics committee review because it is a retrospective analysis of medical records of the veterinary neurology service, school of veterinary medicine and animal science form sao paulo state university-unesp -brazil. not applicable. the authors declare that they have no competing interests. key: cord-270998-1adloi3o authors: cunha, rafes d. s.; da silva junior, camilo l.; costa, camilla a.; de aguiar, hulliana m.; junqueira júnior, danilo g. title: comparison of immunity against canine distemper, adenovirus and parvovirus after vaccination with two multivalent canine vaccines date: 2020-04-27 journal: vet med sci doi: 10.1002/vms3.274 sha: doc_id: 270998 cord_uid: 1adloi3o background: viral diseases are a major cause of morbidity and mortality in puppies. there is a belief among veterinary practitioners and even educational institutions that the vaccines made in brazil against canine distemper virus (cdv), canine parvovirus (cpv) and canine adenovirus (cav) are ineffective or only partially effective. objectives: this study aimed at comparing the immunity of two multivalent vaccines in adult dogs in the city of uberlândia, minas gerais state, brazil. methods: the study was carried out at the animal protection association and a total of 60 adult mongrel dogs were selected and divided into two groups. group a was immunized with two doses of elevencell(®) vaccine and group b received two doses of imported vaccine from the united states; each group was made up of 14 females and 14 males. results: in group a, the elevencell vaccine generated a protective antibody titre against cdv in 26 out of 28 subjects (92.85%), cpv in 24 out of 28 subjects (85.71%) and cav in 26 out of 28 subjects (92.85%). in group b, the imported us vaccine generated a protective antibody titre against cdv in 22 out of 28 subjects (78.57), cpv in 21 out of 28 subjects (75%) and cav in 25 out of 28 subjects (89.28%). there was no statistical difference between titres generated between vaccine types for any of the three diseases tested. conclusion: elevencell vaccine titres were not inferior to the imported us vaccine in conferring protective titres against cdv, cpv and cah, which confirms the efficacy of this product. viral diseases are a major cause of morbidity and mortality in puppies. in this canine population, there is a higher prevalence of canine distemper, parvovirosis and canine infectious hepatitis (vila nova et al., 2018) . these three diseases are aetiologically different, but they can be prevented by vaccination with recombinant or live-attenuated vaccines (day, horzinek, schultz, & squires, 2016) . canine distemper virus (cdv) induces several clinical signs, including fever, dyspnoea, diarrhoea and neurological disorders. these signs may vary according to the host immune status and virus strain. puppies are the most susceptible group to this infection and present the highest fatality rate (martella, elia, & buonavoglia, 2008) . parvoviruses is caused by canine parvovirus type2 (cpv-2), characterized by tropism through rapidly dividing cell lines and affecting dogs at different ages. this disease causes a severe enteric infection with bloody diarrhoea, immune suppression and also high fatality rates. the continuous incidence of enteritis is due to the ability of the virus to mutate, which gives rise to new, more resistant and virulent subspecies (goddard & leisewitz, 2010) . caused by canine adenovirus type1 (cav-1). this virus has tropism for hepatocytes and endothelial cells, which can cause hepatocellular necrosis and systemic bleeding. unvaccinated puppies are the most susceptible to this infection and present non-specific clinical signs, which requires differential diagnosis of other diseases such as canine distemper (decaro, martella, & buonavoglia, 2008 day et al., 2016) . therefore, to choose an appropriate vaccine and the right age for vaccination, it is crucial to seek veterinary advice. there is a belief among veterinary practitioners or even educational institutions that the vaccines made in brazil against cdv, cpv and cav are ineffective or only partially effective. however, there are no published scientific data to support this. a study carried out in viçosa, minas gerais (brazil), showed that the facility where vaccination is performed (veterinary clinics or agricultural stores) is not a determining factor for successful immunization, but rather adherence to the schedule recommended (monti, viana, dias, moraes, & salcedo, 2007) . the lack of research providing a better understanding of the effectiveness of vaccines made in brazil may influence the opinion of clinicians and pet owners when choosing the best immunogen. thus, this study aimed to compare two commercial vaccines, one made in brazil and another coming from abroad, for efficacy against three diseases, namely: canine distemper, parvovirosis and canine infectious hepatitis. this study consisted of a randomized double-blind comparative trial. all procedures were evaluated and approved by the ethics committee on the use of animals at the centro universitário do triângulo (unitri) under the protocol 47/2017-2. the data that support the findings of this study are available on request from the corresponding author. the data are not publicly available due to ethical restrictions. this trial was performed at associação de proteção animal (animal protection association, apa in short) in uberlândia, minas gerais state, brazil. apa, an institution founded in 1996,which has a total of 37 housing units divided into three sectors for dogs, as well as a nursery with 10 housing units for cats and dogs plus two catteries, totalling 300 dogs and about 70 cats. these animals were rescued from the streets, where they had been abandoned, abused or injured. for this study, the criteria for inclusion were animals that had no clinical signs of distemper, parvoviruses and infectious hepatitis, they were dewormed, presented with a medical history inside the shelter (more than a sheltered year) and had negative results in the colorimetric test for the studied antigens. animals with a change in the physical examination, under the age of 3 or over 10 years, less than a year housed or had positive results in the colorimetric test were excluded. a total of 60 dogs were selected (sampling error 12%), half of them males and half females. the animals studied were mongrel adult dogs aged between 3 and 10 years that received the same diet plus water (ad libitum) and were housed in the same housing unit. all animals underwent a thorough physical examination by a veterinarian in order to check for the presence of petechiae, ectoparasites, overt organomegaly and any other abnormalities that could be identified in the examination and interfere with the results. randomization was adopted first stratified by sex, by selecting 30 males and 30 females. then they were separated into blocks of two animals with two sequences of intervention. to guarantee the blinding of the study, the researchers had no contact with vaccines and animals until the moment of the vaccination. the vaccines were stored, prepared and coded by a guest veterinarian who was unaware of the purpose of the experiment. thus, both animals and researchers were blinded for the protocol used in the vaccination. at the end, each group was composed of 15 males and 15 females. group a was given v11 elevencell vac (made in brazil at labovet ® ) and group b received immunization with a vaccine imported from the united states (vangard ® plus, zoetis inc.). one of the vaccines used in this study, brand name v11 elevencell vac, contains live-attenuated virus antigens of distemper, canine parvovirus, infectious hepatitis, adenovirus type2, canine parainfluenza virus, coronavirus-inactivated antigen and five leptospira serovars (l. samples were collected on two occasions: day0 (also known as d0 blood samples were collected from the cephalic or saphenous vein and refrigerated for clot retraction, followed by centrifugation and serum separation. serum was stored at a temperature of −22°c until the tests were performed. all analyses were performed in a clinical laboratory at unitri. the pre-and post-vaccination responses were evaluated using the commercially available kit immunocomb ® (biogal galed labs) based on solid-phase 'dot'-elisa technology and designed for detecting seru-migg or igm levels, validated against gold standard tests: virus neutralization assay(vn) and haemagglutination inhibition assay (hi). in addition, this test kit is a qualitative and quantitative method that provides a diagnosis within 30 min at room temperature (the best results are obtained at a temperature of 20-25ºc) and consists of: (a)a developing plate with 72 wells containing elisa test solutions; (b) an immunocomb card that is inserted in these wells and iminterpretation of the test results according to the manufacturer uses a colour scale from s0 to s6. there are four levels of interpretation:s0, negative; s1-2,inappropriate immunity; ≥s3,positive; ≥s5,strongly positive. all dogs with a reading equal to or higher than s3 were regarded as immunized or protected. the same titre was used for all three diseases. the test presented the following values for specificity (sp) and sensitivity (se): cav, sp 93% and se 94%; cpv, sp 100% and se 88%; cdv, sp 92% and se 100% (biogal galed labs acs ltd., 2016). the cut-point s3 indicates a significant response of anti-cav antibodies (1:16 titre in vn), anti-cpv antibodies (1:80 titre in hi) and anti-cdv antibodies (1:32 titre in vn). the data for the animals were entered individually into excel spreadsheets (version 2013; microsoft corp.). as the procedure is a scale test with a non-normal distribution, the median post-vaccination titre response was obtained, as well as its comparison using the mann-whitney non-parametric test at a significance level of 5%. descriptive statistics were used to calculate the frequencies of animals immunized, and proportions were compared using the binomial test for two proportions at a significance level of 5%. all analyses were carried out using bioestat 5.0 software (ayres, ayres junior, ayres, & santos, 2007). of the 60 animals selected and randomly distributed into two groups, only 56 were analysed because three were adopted during the trial and one died as a result of trauma unrelated to enrolment in the study. thus, each group consisted of 28 dogs. before immunization, both groups of animals presented results of ≤2 on the colorimetric scale, which means that all of them were eligible to take part in the vaccination protocol. when analysing antibody titres against canine distemper, 92.85% (26/28) of the animals of group a were protected (i.e. with a titre of ≥3)and 78.57% (22/28) of group b were protected; thus, there was no significant difference between the groups (p = .12). both groups had a median response of 3.5 on the colorimetric scale and again there was no difference between the groups. a was shown to have a protective titre of ≥3in 85.71% (24/28) and group b in 75% (21/28). there was no statistical difference between the groups (p = .31). both groups had a median response of 4 on the colorimetric scale and again there was no difference between the groups. for analysis of antibody titres against adenovirus, group a was shown to have a protective titre of ≥3in 92.85% (26/28) and group b in 89.28% (25/28); thus, there was no statistical difference (p = .63). group a had a median response of 5.0 for colorimetric titration and group b showed a median response of 4.0. however, these differences were not statistically significant. table 1 shows the frequency of test results for both groups distributed according to the colorimetric scale of the immunocomb ® kit. randomized trials are a powerful tool for reducing bias. by distributing the animals randomly into groups, this ensures uniformity between them. coupled with a double-blind strategy, this helps to avoid any bias that could favour a particular treatment or control (oliveira & parente, 2010) . although no statistical difference between the two vaccines has been shown, a comparable proportion of animals was protected using vaccine v11 made in brazil, which reinforces the quality of the product in comparison to the vaccine imported from the united states. several different factors can affect vaccine induction of a protective titre and may account for the lack of an appropriate response in some animals: factors such as storage conditions, nutritional status of the animal, maternal antibody titres and vaccine immunogenicity (day et al., 2016; monti et al., 2007) . in relation to storage conditions, the vaccines used in this study were stored according to both manufacturers' guidelines and normative instructions (ima, 2012) at a temperature between 2°c and 8°c in a cold chamber, which ensures the quality of the products. another common cause of vaccination failure involves high levels of maternal antibodies, which can inhibit or neutralize the action of the vaccine (nandi, kumar, mohapatra, & ravishankar, 2013) . however, all animals immunized in this study were adults and therefore there was no correlation between vaccination failure and maternal antibody presence. ecto-and endoparasites can also influence the effect of the vaccine because these parasites extract nutrients from the host, causing weakness, anaemia, increased stress and secondary bacterial infections (bowman, lynn, eberhard, & alcarez, 2003) . thirty days before the beginning of vaccination, all animals were given fenbendazole, a broad-spectrum benzimidazole anthelmintic drug used against endoparasites, and also fipronil for the control of ectoparasites. additionally, when selecting the animals for this trial, those that presented with apathy, weight loss, pale mucous membranes, petechiae and ectoparasites were excluded from the study. every effort was made to control any variables that could interfere with the immune response of each animal individually. there were limitations to this study that can be addressed in the future. the absence of public and private funding for execution of the project limited the tests that could be carried out, such as complete blood count, imaging tests to evaluate the spleen and liver and also individual quantification of antibodies by spectrophotometry. both vaccines are effective in the protection of dogs and the v11 elevencell vac made in brazil has been shown to be an appropriate immunogen to induce a strong immune response in a highly challenging environment such as the apa shelter. on behalf of all authors, the corresponding author states that there is no conflict of interest. note: scale: 1-2, inappropriate immunity; 3-4, positive; 5-6, strongly positive. all dogs with a reading equal to or higher than 3 were regarded as immunized or protected. all dogs with a reading of 1 or 2 show the presence of some immune memory cells against the virus tested. manual of infectious hepatitis, parvovirus and distemper igg antibody test kit georgis' parasitology for veterinarians estratégias para vacinação de animais de companhia: cães e gatos wsava guidelines for the vaccination of dogs and cats canine adenoviruses and herpesvirus canine parvovirus. veterinary clinics of north america: small animal practice portaria n°1258 de 18 de outubro de 2012 canine distemper virus anticorpos contra o vírus da cinomose de cães vacinados em diferentes estabelecimentos emergence of canine parvovirus-2 variants and its impact on vaccination understanding randomized controlled trials evaluation of the humoral immune response induced by vaccination for canine distemper and parvovirus: a pilot study key: cord-335087-z1dec19i authors: goldani, luciano z.; salort, shirlei g. title: infectious diseases and the covid-19 scenario in brazil date: 2020-09-06 journal: braz j infect dis doi: 10.1016/j.bjid.2020.07.002 sha: doc_id: 335087 cord_uid: z1dec19i nan arboviruses including dengue, chikungunya, and zika in brazil represent a challenge for public health, considering that are no available vaccines and effective antivirals for treatment. 1, 2 even with the possibility of underreporting, 874,093 probable cases of dengue and 415 deaths have been reported in brazil from january 1 through june 30, 2020. 3 in this scenario, the states of acre, são paulo, paraná, mato grosso do sul, mato grosso, goiás, and distrito federal stand out for presenting higher incidence rates when compared to other locations around the country. according to the general coordination of arbovirus surveillance, denv-2 was the predominant serotype in 79.8% of the samples tested in the country. during the same períod, there were 48,316 probable cases of chikungunya, and 4.666 cases of zika reported in brazil. 3 after launching a mass immunization campaign with a fractional-dose vaccine in 2018, yellow fever was far behind with 881 suspected cases and only 18 confirmed cases reported in the 2019-2020 period. malária remains an important public health problem in brazil because of the high number of cases in the amazonic region. in one year, brazil successfully managed to reduce the number of malaria cases by 23.8%, from 193,837 in 2018 to 156,629 in 2019. 4 this year, the country has been maintaining the reduction, with a 3% drop over the same period in 2019. pan american health organization highlights the need to protect health workers during the covid-19 pandemic, in order to maintain the progress already made in the global fight against malária. as of september 2020, over 4 million cases of covid-19 were reported in brazil, with more than 125.000 deaths. 5 brazil has the second-highest number of confirmed covid-19 cases in the world behind the united states. in addition, 16,638 indigenous citizens were diagnosed with covid-19, and 543 have died according to the national committee of indigenous of life and memory. 6 so far, the coronavirus pandemic has been causing strong impacts and uncertainty on the most diverse spheres of life and business. universities and schools are closed, and it is not clear when they will reopen. brazilś gross domestic product (gdp) was forecast to decrease by 5.95 percent during 2020. 7 8 although current influenza surveillance data should be interpreted with caution, it looks like that influenza activity seems to be at lower levels than expected for this time of the year in brazil. the unified brazilian health system (sus), which already had deficiencies in care for dengue and other diseases, had to adapt abruptly to expand the medical structure and train professionals for the covid-19 pandemic. the impact on the public health system was pronounced by the high demand for hospitalization and health professionals, leading to the depletion of the supply of intensive care beds and pulmonary ventilators in some areas of the country. federal government policies has not promoted social-distancing measures while indicating the antimalarial drug chloroquine as a coronavirus treatment despite a lack of evidence that it is effective. covid-19 testing is being rolled out at an incredibly slow pace, with brazil reporting 7,500 tests per million people, which is almost 10 times less than the us. nevertheless, different scientific organizations, including the brazilian society of infectious diseases, released statements about the use of chloroquine and hydroxychloroquine, describing what science knows about these drugs and criticizing the government's position. efforts to educate practitioners and the public about inappropriate uses of therapeutic drugs were strengthened. the brazilian scientific community is speaking out and producing science related to the pandemic every day. the leaders for two of the most advanced vaccine projects (oxford university, in partnership with astrazeneca, and china's sinovac with butantan institute) will carry out phase 3 tests in brazil. both projects have technology transfer agreements that will enable the country to produce the vaccines themselves, should the tests prove conclusive. as for september 2020, in b r a z j i n f e c t d i s . 2 0 2 0;2 4(4):277-278 pubmed, over 1000 publications were identified by searching terms "covid 2019" and "brazil" in the search field. there is no doubt that fighting against infectious diseases depends upon the establishment of comprehensive plans, appropriate political measures, and science. infectious diseases do not respect borders and require a global response. the availability of powerful new technology tools and ideas makes this an oppurtune time. r e f e r e n c e s dengue and zika: control and antiviral treatment strategies land of choice for arbovirosis? med trop (mars) coordenaç ão-geral de vigilância das arboviroses bol epidemiol especial: doença pelo coronavírus covid-19 bol epidemiol especial: doença pelo coronavírus covid-19 key: cord-337421-4v48kkus authors: ribeiro, servio pontes; dattilo, wesley; castro e silva, alcides; reis, alexandre barbosa; goes-neto, aristoteles; alcantara, luiz; giovanetti, marta; coura-vital, wendel; fernandes, geraldo wilson; azevedo, vasco ariston title: severe airport sanitarian control could slow down the spreading of covid-19 pandemics in brazil date: 2020-03-27 journal: nan doi: 10.1101/2020.03.26.20044370 sha: doc_id: 337421 cord_uid: 4v48kkus background. we investigated a likely scenario of covid-19 spreading in brazil through the complex airport network of the country, for the 90 days after the first national occurrence of the disease. after the confirmation of the first imported cases, the lack of a proper airport entrance control resulted in the infection spreading in a manner directly proportional to the amount of flights reaching each city, following first occurrence of the virus coming from abroad. methodology. we developed a sir (susceptible-infected-recovered) model divided in a metapopulation structure, where cities with airports were demes connected by the number of flights. subsequently, we further explored the role of manaus airport for a rapid entrance of the pandemic into indigenous territories situated in remote places of the amazon region. results. the expansion of the sars-cov-2 virus between cities was fast, directly proportional to the airport closeness centrality within the brazilian air transportation network. there was a clear pattern in the expansion of the pandemic, with a stiff exponential expansion of cases for all cities. the more an airport showed closeness centrality, the greater was its vulnerability to sars-cov-2. conclusions. we discussed the weak pandemic control performance of brazil in comparison with other tropical, developing countries, namely india and nigeria. finally, we proposed measures for containing virus spreading taking into consideration the scenario of high poverty. 1 abstract 2 background. we investigated a likely scenario of covid-19 spreading in brazil 3 through the complex airport network of the country, for the 90 days after the first 4 national occurrence of the disease. after the confirmation of the first imported cases, the 5 lack of a proper airport entrance control resulted in the infection spreading in a manner 6 directly proportional to the amount of flights reaching each city, following first 7 occurrence of the virus coming from abroad. 8 methodology. we developed a sir (susceptible-infected-recovered) model divided in 9 a metapopulation structure, where cities with airports were demes connected by the 10 number of flights. subsequently, we further explored the role of manaus airport for a 11 rapid entrance of the pandemic into indigenous territories situated in remote places of 12 the amazon region. 13 results. the expansion of the sars-cov-2 virus between cities was fast, directly 14 proportional to the airport closeness centrality within the brazilian air transportation 15 network. there was a clear pattern in the expansion of the pandemic, with a stiff 16 exponential expansion of cases for all cities. the more an airport showed closeness 17 centrality, the greater was its vulnerability to sars-cov-2. 18 conclusions. we discussed the weak pandemic control performance of brazil 34 from 17 th to 18 th march, brazil had an increase of 31% in one day, with only four 35 capitals exhibiting community transmission, which was the same to india. however, a 36 very distinct pattern in the ascending starting point for the reported disease exponential 37 curve was observed in each country. by enlarging the comparison to another 38 developing tropical country in the southern hemisphere (thus in the same season), we 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 march 27, 2020. . 39 selected nigeria, since it was the first country to detect a covid-19 case in africa. 40 nigeria displayed less than 10 confirmed cases during the same period of time. 41 furthermore, nigeria has a population (206 million) similar to that of brazil (209 million) . 42 both india and nigeria claim they imposed severe entrance control, and close 43 following up of each confirmed case, as well as their living and working area, and 44 people in contact with them. in brazil, the ministry of health has developed a good 45 monitoring network and a comprehensive preparation of the health system for the worst-46 case scenario. nonetheless, apparently, the decisions from the ministry of health did 47 not cover airport control, and only on march 19 th , eventually too late, the government 48 decided to control the airports, avoiding the entrance of people coming from europe or 49 asia. hence, the entrance of diseased people in brazil has been occurring with no 50 control, at least until the aforementioned date. moreover, after confirming that a person 51 is infected with sars-cov-2, his/her monitoring is initiated but there is no monitoring of 52 his/her living network. 53 for pandemic situations, such as that with which we are living with sars-cov-2, 54 the classical algebraic ecological models of species population growth from verhulst, 55 and species interaction models from lotka-volterra, are theoretical frameworks capable 56 to describe the phenomenon and to propose actions to stop it (pianka 2000) . in many 57 aspects social isolation is a way to severely reduce carrying capacity, i.e., the resources 58 available for the virus dissemination. this is the best action for within-city pandemic 59 spreading of coronavirus (hellewell et al. 2020) , since the main form of transmission is 60 direct contact between people or by contact with fomite, mainly in closed environments, 61 such as classrooms, offices, etc. (rothe et al., 2019; bedford et al., 2020). regardless 62 of virulence, for a highly contagious virus such as sars-cov-2, the occurrence of the 63 first case in a nation will result in a strongly and nearly uncontrollable exponential 64 growth curve, depending only on the number of encounters between infected and 65 susceptible people, and fuelled by a high h0 (the number of people one infected person 66 will infect). 67 on the other hand, the dynamics of disease spreading among cities are entirely 68 distinct. in this work, we present an epidemiological model describing the free entrance 69 of people coming from two highly infected countries with close links to brazil: italy and 70 spain. we showed how sars-cov-2 spreads into the brazilian cities by the 71 international airports, and then to other, less internationally connected cities, through 72 the brazilian airport network. for exploring the dynamics of a continent size, nationwide 73 spreading of sars-cov-2, as it is the case of brazil, we assumed cities connected by 74 airports formed a metapopulation structure. 75 each person in a city was taken as a component of a superorganism, i.e., an 76 interdependent entity where living individuals are not biologically independent between 77 them in various subtle ways. by doing so, we dealt with cities as the sampling units, not 78 the people. flights coming from foreign countries with covid-19 (namely spain and 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 march 27, 2020. . 79 italy for this article) represent the probability of an external invasion of infection in each 80 city. additionally, we also further explored the vulnerability of the amazon region, 81 especially of those remote towns where indigenous and traditional communities 82 predominate. 83 84 materials & methods 85 in order to describe the pattern of air transportation and its role in the spreading of the 86 disease, we built a sir (susceptible-infected-recovered) model (hethcote 1989 ; 87 anderson 1991) split amongst the cities that are interconnected by flights. in this model, 88 the population size inside each city is irrelevant, as well as when the collective infection 89 stage was reached. thus, we assumed that the city was fully infected and became 90 infectious to the whole system, and, therefore, became a source and not a sink of 91 infection events. hence, the sir model started having cities with only susceptible 92 events. infected events only appeared by migration, i.e. travelers only from italy and 93 spain, for sake of simplicity and proximity to the facts. 94 after the first occurrence is registered in the country, infected events started to 95 spread through the national airlines. 96 we used a modified version of the sir model, which took into account the 97 topology of how the cities-demes were linked by domestic flights. in the sir original 98 model, the infection of susceptible cities occurs by probability β of a healthy being (s) 99 encounters an infected one (i). conversely, the model has a probability of an infected 100 one get recovered (r) given by a parameter γ. analytically: (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 march 27, 2020. where k i,j is the number of flights departing at city i and arriving at city j, and α is a newly 132 introduced parameter, which represents the fraction of traveling infected population. for 133 the time, we estimated 90 days for the disease expansion and assumed γ as 0, in other 134 words, no recovery. despite the artificiality of this assumption, we considered that the 135 amount of people still to be infected is larger than those recovered and, thus, becoming 136 resistant, which makes the resistance irrelevant to our output. the model was 137 developed in c and is available as supplementary material 1 (and the database as 138 supplementary material 2). in addition, we also used a linear model to test whether 139 those cities with higher airport closeness centrality (i.e., important cities for connecting 140 different cities within the brazilian air transportation network) were more vulnerable to 141 sars-cov-2 dissemination. 142 143 results 144 the expansion of the sars-cov-2 virus between cities was fast, directly proportional to 145 the airport closeness centrality within the brazilian air transportation network. the 146 disease spread from são paulo and rio de janeiro to the next node-city by the flight 147 network, and in 90 days virtually all the cities with airport(s) were reached, although it 148 occurred with a distinct intensity (figure 2, supplementary material 3) . there was a 149 clear pattern in the expansion of the pandemic, with a stiff exponential expansion of 150 cases (measured as the cumulative percentage of infected people per city) for all the 151 cities. on average, the model showed an ascendant curve starting at day 50 (around 15 152 april), with the most connected cities starting their ascendant curve just after 25 days, 153 and the most isolated ones from day 75 (10th may; figure 3a ). looking at the daily 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 march 27, 2020. . https://doi.org/10.1101/2020.03.26.20044370 doi: medrxiv preprint 154 increment rates, it is clear a first and high peak of infections in the hub cities, happening 155 around 50 days and, starting from 75 days, a new peripheric peak ( figure 3b ). 156 the first ten cities to ascend infection rates (são paulo, rio de janeiro, salvador, 157 recife, brasília, fortaleza, belo horizonte, porto alegre, curitiba, and florianópolis) will 158 actually reach this point about the same time, which is a concerning pattern for the 159 saturation of the public health services. also, this peak in those cities will saturate all the 160 best hospitals in the country simultaneously. 161 therefore, we defined the average proportion of infected people for the 90 days 162 as a measure of vulnerability to covid-19 dissemination. henceforth, we found that 163 more an airport shows closeness centrality within the air transportation network, the 164 greater was its vulnerability to disease transmission (figure 4) . this scenario confirmed 165 the importance of a city connecting different cities within the brazilian air transportation 166 network and, thus, acting as the main driver for the pandemic spreading across the 167 country. 168 169 consequences for the amazonian cities and indigenous people 170 herein we showed that an uncontrolled complex airport system made a whole 171 country vulnerable in few weeks, allowing the virus to reach the most distant and remote 172 places, in the most pessimistic scenario. according to our model, any connected city will 173 be infected after three months. as the number of flights arriving in a city is the driver for 174 the proportion of infected people, manaus, which is a relevant regional clustering, was 175 infected sooner. indeed, on the 17 th of march, manaus was the first amazonian city with 176 confirmed cases (without community transmission yet), and it is a node that is one or 177 two steps to all the amazonian cities. thus, according to our model, manaus may reach 178 1% of the infected population by the 44 th day, while, for instance, the far west 179 amazonian tabatinga will take 61 days to reach the same 1% of the population 180 infected. by day 60, manaus may have an average of 50% of its population infected if 181 nothing is be done to prevent it. tabatinga may also reach the aforementioned value by 182 day 78, if nothing is be done to avoid it. to sum up, within 46 days all the amazonian 183 cities will have 1% of their population infected and a mean of 50% by day 70. 184 185 discussion 186 brazil has failed to contain covid-19 in airports and failed to closely monitor those 187 infected people coming from abroad, as well as their living network. one main reason 188 for this is the difficult logistics required to produce such control in a continental country, 189 such as brazil, which has a complex national flight network. according to the brazilian 190 airport authority, brazil has the second-largest flight network in the world (just after the 191 usa), with a total of 154 airports registered to commercial flights of which 31 are 192 considered international. in comparison, airport control may be much easier to set up in 193 nigeria (31 airports of which only five are international). however, with a population 6.4 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 march 27, 2020. . https://doi.org/10.1101/2020.03.26.20044370 doi: medrxiv preprint 234 network of brazil, which is also key for the whole latin america, if not properly 235 monitored and controlled, may cause a window of opportunity for the virus to spread 236 over the entire continent. 237 the consequences of this uncontrolled sars-cov-2 spreading is particularly 238 serious if one takes into consideration the chances of a mutant virulent strain appearing 239 and spreading into poorer and little monitored places of the world. specifically, for the 240 amazon region, the lack of any control will make the city of manaus a very sensitive 241 cluster for public health, due to predominantly poor and indigenous-dominated cities in 242 the region, which are connected to manaus and will be rapidly infected. reaching 243 isolated regions means reaching indigenous or traditional communities, whose 244 individuals are classically more susceptible to new pathogens than western-influenced 245 or mixed urban populations. therefore, a way to prevent such spreading, if still there is 246 time, would be to deal with airports as entrances that need severe infection barriers. the eventual lesson to take is that inflexible, severe, and easy to repeat 250 controlling protocols must be applied to all the cities with airports. likewise, the follow-251 up monitoring of suspicious individuals and their living network should be reinforced as 252 a national strategy to prevent a large territory to be taken over by a pandemic in a short 253 period of time. in other words, internationally accepted procedures must be taken and 254 even be reviewed to adjust to complex national flight networks of any country. such 255 procedures must be considered as a priority for national remote airports too, in order to 256 keep poorer and worse equipped cities away from a rapid spread of a pandemic 257 disease. 258 it is clear at this point that a fast spread of the sars-cov-2 is a reality in brazil, 259 and across most of the country. we proposed this model in order to emphasize the 260 fragility of brazilian surveillance in the airport network, in an attempt to cause some 261 policy change in time to preserve at least the most remote regions, which are also the 262 most vulnerable, with a weaker health service. moreover, most of the eastern part of the 263 country must stay in social isolation in order to prevent a health public collapse by mid-264 april, as the ministry of health predicted. in addition, we also could consider the 265 generalized poverty of brazil as a further problem our model did not deal with. the 266 chances to produce home-to-home isolation, even legally imposed, is impossible for 267 these poor communities. nonetheless, considering the few main entrances of most of 268 the brazilian shanty towns and communities, a similar to airport entrance severe control 269 must be considered to protect a larger but closely connected set of people, eventually 270 following the protocols used for control of ebola during the last epidemic in africa (lau 271 et al. 2017 ). 272 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 march 27, 2020. than brazil, india, in turn, has a similar sized airport network to brazil nevertheless, the situation of covid-19 in india is currently much milder than in besides the within-city pattern of virus spreading, one must take into account the 205 pattern of dispersion between cities after the virus has invaded. additionally, for the 206 brazilian case 3 million in salvador where the brazilian ministry of tourism revealed 210 that 86,000 foreigners from france considering a disease with so many asymptomatic cases, it could have invaded before 212 but, with the lack of an early warning and airport control, one will never know exactly if the lack of control for these situations may result in a 218 dramatic rate of host infection, and an eventual collapse of the host-parasite interaction 219 in a given population, depending on the amount of susceptible, infected and recovered 220 events. nonetheless, if the population is split into deme-cities, in a metapopulation 221 structure, the collapse takes longer, and a much greater amount of people in different 222 locations may eventually be infected, as found in our model. it is worthwhile to mention 223 that this model, already pessimistic, did not consider the road network, one of the 224 largest on the planet. most importantly, the best road-connected cities are exactly those 225 mostly connected by airport, and that will be vulnerable earlier, thus, probably spreading commercial flights, very common in the amazonian and 229 western regions. taking this into a global scale we thank christina vinson and thomas c.a. williams for the english revision cnpq agency guarantee research grant scholarship to spr discussion: the kermack-mckendrick epidemic threshold 283 theorem lancet covid-19: towards controlling of a pandemic. the 285 lancet ecological and immunological 287 determinants of influenza evolution feasibility of controlling covid-19 outbreaks by 290 isolation of cases and contacts three basic epidemiological models spatial and temporal dynamics of superspreading 295 events in the 2014-2015 west africa ebola epidemic simple mathematical models with very complicated dynamics prediction and prevention of 300 the next pandemic zoonosis evolutionary ecology, 6 th edition transmission of 2019-ncov 304 infection from an asymptomatic contact in germany figure 2 -proportion of infected population of each brazilian city in 40 after initiating all variables to an initial condition, that 335 is, s (health), i (infected) and r (recovered) of each city, the code starts loading the network 336 and calculates the total number of flights among all the cities. this information is used to feed 337 the classical sir model introducing in the variable i, the information regarding infected travelers 338 and non-travelers 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 key: cord-345238-p841weif authors: magalhaes, tereza; chalegre, karlos diogo m.; braga, cynthia; foy, brian d. title: the endless challenges of arboviral diseases in brazil date: 2020-05-09 journal: trop med infect dis doi: 10.3390/tropicalmed5020075 sha: doc_id: 345238 cord_uid: p841weif in this editorial, we list and discuss some of the main challenges faced by the population and public health authorities in brazil concerning arbovirus infections, including the occurrence of concurrent epidemics like the ongoing sars-cov-2/covid-19 pandemic. the cross-reactivity between denv and zikv serological assays are due to similar antigenic regions of viral proteins of these genetically related flaviviruses that can be recognized by the same antibodies. besides being an issue in serological tests, cross-reactive denv and zikv immunity can have important epidemiological implications in places where these viruses co-circulate. for instance, in vitro, in vivo and epidemiological studies have shown that pre-existing denv immunity can either protect or enhance zikv infection, and consequently impact disease development [4] [5] [6] . other studies suggest that the atypically low dengue incidence observed after the zika epidemics in brazil and other latin american countries was due, in part, to short-term denv protection from zikv infections [7, 8] . importantly, this lower dengue incidence was followed by a significant increase in dengue cases [2, 7] . the impact of pre-existing denv and zikv immunity in further heterologous infections and, importantly, in clinical diseases, needs to be continuously assessed in endemic areas. it is also possible that zikv or other arboviruses may establish sylvatic transmission cycles in brazil, as discussed by other authors [9] . if one looks at the map of paulista, for example, a municipality within the recife metropolitan region (rmr) in pernambuco state that was heavily affected by zikv and chikv, forested areas surround all the urban areas where the viruses co-circulated and human cases were concentrated in 2015-16 ( figure 1 and [10] ). these forested areas may harbor several sylvatic mosquitoes like aedes albopictus, haemagogus janthinomys, and sabethes tarsopus that feed on non-human primates (nhps) and may serve as vectors of arboviruses [11] . in addition, nhps like the common marmoset callithrix jacchus are abundant in the area [12] and found near humans. importantly, zikv rna and antibodies against several arboviruses have been found in nhps in different regions of brazil, including marmosets [13] [14] [15] [16] . the seriousness of an established sylvatic arbovirus transmission cycle in nhps and sylvatic mosquitoes in brazil is well represented by yellow fever virus (yfv), which causes sporadic spillover human outbreaks leading to hundreds of deaths. although a few studies have found little evidence of sylvatic zikv transmission in brazil [16, 17] , the possibility of a sylvatic cycle being established in distinct brazilian regions and at different times cannot be excluded. further governmental or research-related arbovirus surveillance activities should intensify monitoring of sylvatic mosquitoes, nhps and other small mammals, as the establishment of sylvatic cycles will require changes in the design of control programs. the zikv outbreaks that occurred in brazil in 2014-16 probably ceased due to herd immunity-however, instead of disappearing, the virus is still circulating in areas that were intensely affected, like the rmr, even if at low rates. in addition, virus transmission during the outbreaks was focal across metropolitan regions, where some areas were more intensely hit than others within the same municipality [4] , corroborating the notion of clustered household/community transmission of arboviruses transmitted by ae. aegypti. the low but constant circulation of zikv, the presence of prior virus foci with surrounding patchy areas containing higher numbers of naïve people, and the possibility of a sylvatic cycle being established in some regions increase the chances of unexpected re-emergence of the virus. it will also be important to assess the importance of sexual transmission among the sustained, low zikv circulation in endemic regions, as the epidemiological relevance of zikv sexual transmission may be higher than previously thought ( [18] and magalhaes et al., unpublished) . escalating the problem of arboviral disease surveillance and management, concurrent outbreaks/epidemics of arboviruses and non-arthropod-borne pathogens can further complicate clinical diagnosis and completely overwhelm/saturate the health care system, as we may be seeing now with the pandemic of coronavirus disease (covid-19) caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2). the number of notified dengue, zika and chikungunya cases in brazil in 2020 have reached over 660,000 by april [2], reflecting a difficult year for arboviral diseases in the country (figure 2a ). although the true incidences of sars-cov-2 infections and covid-19 cases are unknown in brazil due to the very limited testing (currently, the brazilian government recommends that only severe cases are tested in health clinics and hospitals), the notified numbers of infections and deaths are starting to increase, indicating a worsening epidemic scenario as of april 2020 ( figure 2b) [2]. at the moment, health care units like the local rapid-access units (unidades de pronto atendimento-upas), which serve communities like the paulista population (~330,000 habitants), are working with a reduced number of staff as some individuals have fallen ill and many elderly professionals or those with comorbidities are on leave due to fear of becoming infected with the virus. in a recent serosurvey of sars-cov-2 antibodies among health professionals in pernambuco state, 60% have tested positive, confirming these professionals are under very high risk of infection [19] . although the highest numbers of notified arboviral diseases seemed to have occurred in march 2020, it is very likely that case notification has dropped as a result of fewer people infected with arboviruses seeking health facilities due to the sars-cov-2 pandemic. in fact, it would be important to see if household mosquito transmission of arboviruses increases because of social isolation during the covid-19 pandemic, considering the endophilic behavior of ae. aegypti (although social isolation is necessary, it is also important to assess its effects on other health factors). the blunt reality is that health care units have been dealing with a peak in arbovirus infections and covid-19 cases concomitantly. besides the many troubles inherent to an overwhelmed health care system, concurrent epidemics also can complicate clinical-epidemiological diagnoses. some studies show that dengue cases can be misdiagnosed as respiratory infections and vice-versa [20, 21] . coinfections during concurrent epidemics must also be considered as they may worsen clinical diseases. coinfections of influenza virus and denv have been identified in several occasions during concurrent epidemics [22] [23] [24] . future control efforts and programs must consider concurrent epidemics as they will most likely continue to happen in the future (e.g., epidemics of denv and new strains of influenza virus). areas where cases were concentrated: an optimal interface for the establishment of sylvatic cycles of arbovirus transmission (this map was published in [10] ). effective management of arboviral diseases in brazil requires confronting major challenges. the co-endemicity of multiple and related arboviruses complicates clinical-epidemiological diagnoses, clinical management and case notification, in addition to impacting the epidemiology of arboviral diseases in unclear ways. the possible establishment of sylvatic transmission cycles will represent a significant additional challenge to the development of control programs and should be constantly monitored. lastly, concurrent epidemics like the sars-cov-2/covid-19 or other respiratory pathogens/illnesses can overwhelm health care systems and further complicate clinicalepidemiological diagnoses. efforts to better control these diseases must seriously consider all these issues. the authors declare no conflict of interest. brito effective management of arboviral diseases in brazil requires confronting major challenges. the co-endemicity of multiple and related arboviruses complicates clinical-epidemiological diagnoses, clinical management and case notification, in addition to impacting the epidemiology of arboviral diseases in unclear ways. the possible establishment of sylvatic transmission cycles will represent a significant additional challenge to the development of control programs and should be constantly monitored. lastly, concurrent epidemics like the sars-cov-2/covid-19 or other respiratory pathogens/illnesses can overwhelm health care systems and further complicate clinical-epidemiological diagnoses. efforts to better control these diseases must seriously consider all these issues. the authors declare no conflict of interest. one year after the zika virus outbreak in brazil: from hypotheses to evidence serological tests reveal significant cross-reactive human antibody responses to zika and dengue viruses in the mexican population impact of preexisting dengue immunity on zika virus emergence in a dengue endemic region previous dengue or zika virus exposure can drive to infection enhancement or neutralisation of other flaviviruses dengue virus and zika virus serological cross-reactivity and their impact on pathogenesis in mice impacts of zika emergence in latin america on endemic dengue transmission the decline of dengue in the americas in 2017: discussion of multiple hypotheses human urban arboviruses can infect wild animals and jump to sylvatic maintenance cycles in south america a list of mosquito species of the brazilian state of pernambuco, including the first report of haemagogus janthinomys (diptera: culicidae), yellow fever vector and 14 other species (diptera: culicidae) spatial distribution and exploitation of trees gouged by common marmosets (callithrix jacchus) evidence of natural zika virus infection in neotropical non-human primates in brazil seroprevalence of selected flaviviruses in free-living and captive capuchin monkeys in the state of pernambuco limited evidence for infection of urban and peri-urban nonhuman primates with zika and chikungunya viruses in brazil zika virus surveillance at the human-animal interface in west-central brazil prevalence and incidence of zika virus infection among household contacts of patients with zika virus disease influenza illness among case-patients hospitalized for suspected dengue frequency and clinical features of dengue infection in a schoolchildren cohort from medellin, colombia severe coinfections of dengue and pandemic influenza a h1n1 viruses co-infection with dengue virus and pandemic (h1n1) 2009 virus the diagnostic challenge of pandemic h1n1 2009 virus in a dengue-endemic region: a case report of combined infection in jeddah, kingdom of saudi arabia this article is an open access article distributed under the terms and conditions of the creative commons attribution (cc by) license key: cord-270519-orh8fd1c authors: oliveira, a. c. s. d.; morita, l. h. m.; da silva, e. b.; granzotto, d. c. t.; zardo, l. a. r.; fontes, c. j. f. title: bayesian modeling of covid-19 cases with a correction to account for under-reported cases date: 2020-05-25 journal: nan doi: 10.1101/2020.05.24.20112029 sha: doc_id: 270519 cord_uid: orh8fd1c the novel of covid-19 disease started in late 2019 making the worldwide governments came across a high number of critical and death cases, beyond constant fear of the collapse in their health systems. since the beginning of the pandemic, researchers and authorities are mainly concerned with carrying out quantitative studies (modeling and predictions) overcoming the scarcity of tests that lead us to underreporting cases. to address these issues, we introduce a bayesian approach to the sir model with correction for under-reporting in the analysis of covid-19 cases in brazil. the proposed model was enforced to obtain estimates of important quantities such as the reproductive rate and the average infection period, along with the more likely date when the pandemic peak may occur. several under-reporting scenarios were considered in the simulation study, showing how impacting is the lack of information in the modeling. the covid-19 epidemic disease is caused by the new sars-cov-2 coronavirus associated with the severe acute respiratory syndrome (sars) that began in wuhan, china, late 2019 (rodríguez-morales et al., 2020) . after the first detected case in china, the disease continued to spread globally with exported cases confirmed in all of the continents worldwide. in a matter of a few months, the disease overtook 80 thousand reported cases until early april, 2020. on march 12nd, 2020 the world health organization (who) declared covid-19 as pandemic disease, when more than 20 thousand cases and almost a thousand deaths were registered in the european region -the center of this pandemic according to the europe's standing committee (who, 2020) . there are still many unknowns about covid-19 and the lack of evidence complicates the design of appropriate response policies -for example, it is impossible to precisely say something about the mortality rate and determine the disease recurrence rate (lenzer, 2020) . despite uncertainties, the frightening speed through which this disease spreads across communities and the collapse that it is capable of causing to the health systems are facts that must be faced. the exponential growth of the cases and the consequent number of deaths had been observed in a short period. in mid-january 2020, a few weeks after the first detected covid-19 case in the world, the countries that are close to the territory of the virus origin, on the asian continent, as well in european and american regions also began to report cases of the disease. five months later, more than 200 countries and territories around the world have reported over to 3 million confirmed cases of covid-19 and a death toll of about 200 thousand people. in brazil, the first confirmed covid-19 case occurred on february 25th, 2020. this first case was a 61 years-old male, who stayed from february 9th to february 20th, 2020 in lombardy -an italian region were a significant outbreak was ongoing at that time. on march 17th, the health authorities in são paulo confirmed the brazilian death from the new coronavirus. the victim, whose identity has not been disclosed, had been hospitalized in são paulo city. preserving due proportions, covid-19 is not the first experienced significant outbreaks of infections that were declared public health emergencies of international concern by the who. year after year we also have experimented with the zika and chikungunya outbreaks in the last decade and continue facing the huge consequences of dengue. confronting outbreaks in the large brazilian territory is a twofold problem. the first is the demographic and territorial size of the country, with an estimated population of 210 million according to the brazilian institute for geography and statistics and the heterogeneity intrinsic to its extensive territory. another problem pointed out by the past epidemics run into a recurring problem of under-reporting (de oliveira et al., 2017; stoner et al., 2019) . the covid-19, given its complexity and behavior, exposed the problem of under-reporting disease occurrence not only in brazil but in several countries worldwide. as a consequence, the lack of information has launched a warning about the researchers of the world concerning models and estimates, since the database available may not be reliable from what had indeed been observed. focusing on the modeling and estimating, aiming to preview the behavior and the speed of the covid-19 growth, this paper presents an approach to address the problem of under-registration of covid-19 cases in brazil, proposing methodologies to work on the inaccuracy of the official reported cases. then, we investigate a general framework for correcting under-reporting data making it possible to perform a model, in a bayesian framework, which allows great flexibility and leads to complete predictive distributions for the true counts, therefore quantifying the uncertainty in correcting the under-reporting. several scenarios of under-reporting were considered in a simulation study, presenting the real lack of data impact. this paper is organized as follows. section 2 describes the methodology for estimating the reported rates. in section 3, we introduce the sir model for modeling epidemics. in section 4, we introduce the bayesian framework for the sir model with a modification to account for under-reporting. in section 5 we show the model application for covid-19 cases in brazil and in section 6, we present a simulation study of the proposed model. finally, in section 7, we give some concluding remarks. although in the first moment there was a real hunt for the size and the moment of the covid-19 cases peak, the most important aspects of the outbreak are the growth rate of the infection. statistical and mathematical models are being used to preview the rates and analyze the growth curve behavior to assist health public managers in decision-making (cotta et al., 2020) . according to kim et al. (2020) , estimating the case fatality rate (cfr) is a high priority in response to this pandemic. this fatality rate is the proportion of deaths among all confirmed patients with the disease, which has been used to assess and compare the severity of the epidemic between countries. the rates can also be used to assess the healthcare capacity in response to the outbreak. indeed, several researchers are interested in estimating the cfr in the peak of the outbreak, analyzing its variation among different countries, and check the influence of other features as ages, gender, and physical characteristics in the cfr of the covid-19. aiming to estimate the cfr, first of all, lets set up the brazilian scenario of covid-19 case notification: the brazilian ministry of health collects daily all confirmed cases data for brazil and all its states. although the data presented by the health authorities are official, they are only from patients with covid-19 confirmed by blood and/or swab positive tests. given the scarcity of tests for all the suspected individuals, the notified patients are only those with severe disease or that demanding hospitalization. it is relevant to highlight that no clinically diagnosed patient, even those with symptoms compatible with the disease have been officially counted, evidencing an under-reporting of the case frequency. faced with the lack of covid-19 tests, which naturally leads to the underreporting data, before any modeling purpose we have the desire to correct and update the current numbers, bringing them as close as possible to reality. following russel et al. (2020) , we also based on a delay-adjusted case fatality ratio to estimate under-reporting, using the incidence of cases and deaths to estimate the number of notified cases by where c t is the daily incidence of cases at the moment t, f j is the proportion of cases with a delay between the confirmation and the death, and µ t represents the underestimation proportion of cases with known outcomes, (nishiura et al., 2009) . then, the corrected cfr is given by where m t is the cumulative number of deaths. to estimate the potential for under-reporting, we assume that the cfr is 1.4% with a 95% confidence interval from 1.2% up to 1.7% found in china (guan w-j, 2020) . thus, the potential for reporting rate is given by (3) epidemic models are tools widely used to study the mechanisms by which diseases spread, to predict the course of an outbreak, and to evaluate strategies to control an epidemic disease. several analyses of an epidemic spreading disease can be found in the literature that applies the time series model (given the historical data), the log-logistic family of models (the chapman, richards, among others), and compartments models (bjørnstad, 2018). kermack & mckendrick (1927) proposed a class of compartmental models that simplified the mathematical modeling of infectious disease transmission. entitled as sir model, it is a set of general equations which explains the dynamics of an infectious disease spreading through a susceptible population. essentially, the standard sir model is a set of differential equations that can suit the susceptible (if previously unexposed to the pathogen), infected (if currently colonized by the pathogen), and removed (either by death or recovery) as follows: where s, i and r are the total number of susceptible, infected and removed individuals in the population, respectively, γ is the removal rate and β is the infectious contact rate. it is important to note that and so, the total population, s(t) + i(t) + r(t) remains constant for all t ≥ 0. 4 . 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 25, 2020. . for the practical point of view, the most interesting issue is to estimate 1 γ , which determines the average infection period and the basic reproductive ratio r 0 = β γ , defined as the expected number of secondary infections from a single index case in a completely susceptible population (keeling & rohani, 2011) . the bayesian methods are used in several works (gelman et al., 1995) ; (paulino et al., 2018) . the bayesian approach in the context of the sir model is a flexible way to account for uncertainty in the parameters, in the form of the disease transmission dynamic. the dirichlet-beta state-space model appears in some papers as osthus et al. (2017) and song et al. (2020) . the target distribution for inference is the a posteriori distribution of the quantities of interest, more specifically β, γ, and r 0 : the infectious contact rate, the removal rate, and the propagation rate, respectively. the application of this methodology is through markov chain monte carlo methods (mcmc) through gibbs sampling and the metropolis-hastings algorithm (chib & greenberg, 1995) . the use of dirichlet distribution for the proportions of susceptible, infected, and removed individuals in the target population are a feasible way to guarantee that the support set of these quantities has boundaries, for example, the number of infected individuals must be always positive. in this section, we present a modification to account for under-reporting in the context of the dirichlet-beta state-space model from osthus et al. (2017) . this adaptation is based on a reparametrization of beta distribution that includes the reported rate estimate, η, from equation (3). the beta distribution, as is well known, is very flexible for proportions modeling since its density can have quite different shapes depending on the values of the two parameters that index this distribution (ferrari & cribari-neto, 2004) . for this reason, we made a reparametrization to the beta model in such a way that we could obtain a regression structure for the means of the response variables associated with a precision parameter. let y i t be the reported infected proportion, y r t be the reported removed proportion and θ t = (θ s t , θ i t , θ r t ) be the true but unobservable susceptible, infectious, and removed proportions of the population, respectively. hence, we rewrite the sir model in terms of these unobservable proportions as the following 5 . 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 25, 2020. . https://doi.org/10. 1101 then, the distributions for y i t , y r t , and θ t are given below where φ = (β, γ, θ 0 , κ, λ) is the parameter vector for this model and f (θ t−1 , β, γ) is the solution for the differential equations in (4). note that it is necessary to obtain the solutions for the proportions θ s t θ i t and θ r t . these solutions can be found using the runge-kutta fourth-order method, in short rk4, for solving non-linear ordinary differential equations (mathews, 1992) and can be seen in appendix a. the official brazilian data consists of daily collections carried out by the national health department with records of infected individuals and deaths in all states and national territory, from february 26th, 2020 when the first case of covid-19 was registered up to may 20th, 2020. it is notable in brazil a lack of testing due to the registry of only severe cases and consequently under-reporting cases of covid-19. taking this fact into account, we consider for this research not only the official data but also the estimates of reported rate. in order to obtain the estimate of reported rate, assume that the delay in confirmation until death follows the same estimated distribution of hospitalization until death. using data from covid-19 in wuhan, china, between december 17th, 2019, and january 22nd, 2020, it has a lognormal distribution with mean of 13, median of 9.1 and standard deviation of 12.7 days (linton nm, 2020) . this methodology based on the information of delay from hospitalization until death is reasonable since china was considered as one of the countries that most tested the population for the virus, and consequently, it is supposed to have a tiny under-reporting rate. using the methodology presented in section 2, the reporting rate in brazil, η, was estimated to be 0.07 with 95% confidence interval from 0.06 up to 0.08. prado et al. (2020) obtained a reporting rate of 0.08 with data from brazil until april 10th, 2020. these results are similar to the analysis from ribeiro & bernardes (2020) , which present a 7.7 : 1 under-reporting rate, meaning that the real cases in brazil should be, at least, seven times the published number. table 1 presents the rates for all states of brazil, from which we can observe that paraíba has the lowest reported rate 0.06 and while roraima presents the highest reported rate 0.52. indeed, prado et al. (2020) found that paraíba and pernambuco had a low reporting rate comparing with other states. . 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 25, 2020. . https://doi.org/10.1101/2020.05.24.20112029 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 this version posted may 25, 2020 . . https://doi.org/10.1101 for the adjustment of the bayesian model, the prioris and hyper-parameters are specified: γ -we assume that the average infection period is equal to 15 days. thus, the γ a priori belongs to lognormal distribution with mean of 0.07 and variance of 0.01. γ ∼ logn(−3.215, 1.112). the average infection period ρ comes directly from γ parameter, that is, ρ = 1 γ . β -the reproduction number r 0 of the disease is estimated by the ratio r 0 = β γ . we assume that r 0 a priori belongs to lognormal distribution with mean of 3 and variance of 9. thus β values were obtained from the a priori distributions for k, λ i and λ r and θ 0 were obtained according to osthus et al. (2017) , that is, the estimates from a posteriori distributions for r 0 , β, γ, k, λ i and λ r were obtained through mcmc methods, specifically gibbs sampling (geman & geman, 1984) . to execute the sampling procedure, we used the r programming language (r core team, 2020), with rjags package (plummer, 2019) . the total number of iterations considered, as well as the discard (burn-in) and the minimum distance between one iteration to another (thin) were obtained through the criterion of raftery & lewis (1992) in the analysis of a pilot sample with 10,000 iterations. the convergence diagnosis of the mcmc procedure was verified using the geweke (geweke, 1992) and heidelberger and welch(heidelberger & welch, 1983) criteria, which are available in the coda package (plummer et al., 2006) . table 2 shows the p-values from geweke, and heidelberger and welch convergence diagnostics, from which we conclude that chains reached convergence for all parameters (p-value > 0.05). the inference was made by considering the reported rate estimate in brazil,η = 0.07, a chain of 300,000 interactions was generated, with a burn-in of 10,000 and a thin of 300, resulting in a final sample of 1,450 values. the parameter estimates are shown in table 3 , in whichβ = 0.1125 and γ = 0.0308 are the major characteristics from sir model andk = 52, 535.34, λ i = 217, 894.30 andλ r = 223, 431.60 express the magnitude of the process error for the unknown proportions (θ) in bayesian approach. 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 this version posted may 25, 2020. . https://doi.org/10.1101/2020.05.24.20112029 doi: medrxiv preprint the inference results show thatr 0 = 3.6243 which expresses a high reproductive rate of the virus. also,ρ = 32.1667 days shows that the time for virus infection is very close to one month period. using the parameter estimates from table 3 and the latent proportion (θ), we reached information about the peak from sir curve for the covid-19 transmission in brazil, that is the time when the proportion of infected individuals reaches its maximum. the peak estimate is june 18th, 2020, occurring between june 12nd and june 22th, 2020 and it is shown in figure 1 . concerning to evaluate the effect of the notification rate on the model's estimates, a simulation study was carried out. the model was estimated considering covid-19 data in brazil, assuming a reporting rate between 0.05 and 1.00, varying every 0.05. aiming the practical point of view, we conduct a simulation study to investigate the effects of under-reporting in the parameters of the sir model and how it impacts on the pandemic curve behavior. for each value of η, a chain of 300,000 interactions was generated, with a burn-in of 10,000 and a thin of 300. figure 2 shows the point estimates and 95% credible intervals for β and γ versus the reported rate values. it can be observed that as reported rate increases, β estimate becomes lower, which means that the infectious contact rate 9 . 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 25, 2020 may 25, . . https://doi.org/10.1101 may 25, /2020 doi: medrxiv preprint is underestimated when under-reporting is ignored. additionaly, the removal rate γ remains almost constant when the reported rate increases, which means that it is not influenced by the rates. the graphics with the point estimates and 95% credible intervals for r 0 and infection period ρ versus the reported rates are shown in figure 3 , from which we observe that r 0 decreases as the reported rate increases and ρ keeps roughly invariant, then we can conclude that the reproduction rate and infection period can be underestimated when under-reporting is ignored, affording an unreal impression on a tiny mean number of secondary individuals that a primary individual can infect, when in fact it is large. figure 4 shows the estimated sir curves for covid-19 versus reported rate, from which we observe that the lower the reported rate, the earlier the peak is reached with a higher proportion of infected individuals. it is also observed that the contagion curves become similar to each other as the reported rates increase. these results reveal that the peak estimate of the covid-19 transmission curve 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 this version posted may 25, 2020. . https://doi.org/10.1101/2020.05.24.20112029 doi: medrxiv preprint in brazil is compromised when the presence of under-reporting is ignored. finally, table 4 presents the deviance information criterion (dic) (spiegelhalter et al., 2002) , which indicates the sir model with the reported rate of 0.1 as the best one that fitted the simulated data, since its dic value is the lowest. these results suggest that the notification rate is very low. in this paper, we show that the method of adjusting cases by delay can be used to determine the reported rate of covid-19 cases. thus, it was possible that the rate of cases reported in brazil is 0.07 and thus underestimates the real spreading of pandemic in the country. thus we proposed a sir model with correction for under-reporting. the bayesian approach is a feasible way to deal with the parameters inherent to the sir model. . 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 25, 2020. . https://doi.org/10.1101/2020.05.24.20112029 doi: medrxiv preprint the methods reached convergence in the application with the brazilian covid-19 data set. thus, a reproductive rate of 3.6243 was obtained, indicating that the epidemic is still booming in brazil. the simulation study revealed that the parameters estimates from the sir model and the peak estimate which is a concern of several researchers and health authorities are sensitive to reporting rates. future work may include considering the use of extended sir models like the seir model (with the compartments of susceptible, exposed, infected, and removed individuals), and further, consider different scenarios of isolation and quarantine for the strategy of the covid-19 transmission control. , o. n. (2018) . epidemics: models and data using r. springer. chib, s., & greenberg, e. (1995) . understanding the metropolis-hastings algorithm. the american statistician, 49 , 327-335. url: http://www.jstor. org/stable/2684568. cotta, r. m., naveira-cotta, c. p., & magal, p. (2020). parametric identification and public health measures influence on the covid-19 epidemic evolution in brazil. medrxiv , . arxiv:https://www.medrxiv.org/content/early/2020/05/12/2020.03.31.20049130.full.pdf. 12 . 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 25, 2020. . https://doi.org/10.1101/2020.05.24.20112029 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. (which was not certified by peer review) the copyright holder for this preprint this version posted may 25, 2020 . . https://doi.org/10.1101 evaluating the accuracy of sampling-based approaches to the calculation of posterior moments clinical characteristics of coronavirus disease 2019 in china simulation run length control in the presence of an initial transient modeling infectious diseases in humans and animals containing papers of a mathematical and physical character understanding and interpretation of case fatality rate of coronavirus disease 2019 covid-19: us gives emergency approval to hydroxychloroquine despite lack of evidence incubation period and other epidemiological characteristics of 2019 novel coronavirus infections with right truncation: a statistical analysis of publicly available case data numerical methods for mathematics, science and engineering early epidemiological assessment of the virulence of emerging infectious diseases: a case study of an influenza pandemic a random-censoring poisson model for underreported data forecasting seasonal influenza with a state-space sir model lisboa: fundação calouste gulbenkian rjags: bayesian graphical models using mcmc coda: convergence diagnosis and output analysis for mcmc análise de subnotificação do número de casos confirmados da covid-19 no brasil r: a language and environment for statistical computing. r foundation for statistical computing comment: one long run with diagnostics: implementation strategies for markov chain monte carlo estimate of underreporting of covid-19 in brazil by acute respiratory syndrome hospitalization reports going global-travel and the 2019 novel coronavirus. travel medicine and infectious disease using a delay-adjusted case fatality ratio to estimate under-reporting. available at the centre for mathematical modelling of infectious diseases repository, here an epidemiological forecast model and software assessing interventions on covid-19 epidemic in china. medrxiv bayesian measures of model complexity and fit a hierarchical framework for correcting under-reporting in count data who announces covid-19 outbreak a pandemic let f (θ t−1 , β, γ) be the runge-kutta rk4 approximation to the sir model. thus, key: cord-262003-vjqqtqd6 authors: dutra, j. c. s.; da silva, w. b.; da costa, j. m. j. title: monitoring and forecasting the number of reported and unreported cases of the covid-19 epidemic in brazil using particle filter date: 2020-05-29 journal: nan doi: 10.1101/2020.05.27.20115212 sha: doc_id: 262003 cord_uid: vjqqtqd6 in this paper, we combine algorithm of liu & west for the particle filter (pf) with siru-type epidemic model to monitor and forecast cases of covid-19 in brazil from february up to september. we filter the number of cumulative reported cases and estimate model parameters and more importantly unreported infectious cases (asymptomatic and symptomatic infectious individuals). the parameters under study are related to the attenuation factor of the transmission rate and the fraction of asymptomatic infectious becoming reported as symptomatic infectious. initially, the problem is analysed through particle swarm optimization (pso) based simulations to provide initial guesses, which are then refined by means of pf simulations. subsequently, two additional steps are performed to verify the capability of the adjusted model to predict and forecast new cases. according to the results, the pandemic peak is expected to take place in mid-june 2020 with about 25,000 news cases per day. as medical and hospital resources are limited, this result shows that public health interventions are essential and should not be relaxed prematurely, so that the coronavirus pandemic is controlled and conditions are available for the treatment of the most severe cases. the first infection by the new coronavirus (sars-cov-2) was detected on december 31, 2019, in wuhan, china and a pandemic was declared by the world health organization on march 11, 2020 [1, 2] . such infection causes the covid-19, whose main symptoms include cough, fever, difficulty breathing. it presented a scary evolution with millions of infected people and thousands of deaths in the world. because these facts, the affected countries and cities around the world have been reacting in different ways, towards locally controlling the disease evolution. in brazil, the first case of covid-19 was confirmed on february 26, 2020. ever since, the number has surged to more than 310,000 cases of the disease, according to the brazilian ministry of health [3] . such milestone makes this nation to become the third one with the highest number of infections in the world, behind only the united states and russia. specifically, amazonas, ceara, pernambuco, rio de janeiro and sao paulo have been the worst affected states in brazil, whose cases correspond to at least 60% of all cases in the country. the coronavirus has so far been responsible for more than 20,000 deaths. on may 21, 2020, an unenviable record was broken with 1,188 new deaths reported officially within a single day. this acceleration of the pandemic shows that brazil tends to become a new global epicentre of the covid-19 [4] . figure 1 comprising data up to may 21, 2020 shows that the number of confirmed cases of the covid-19 in brazil has significantly exceeded the number of cases in china. this extent of the disease reveals a dramatic situation, since the population of brazil is approximately 6.5 times smaller than that of china, which implies the urgent need for epidemiological studies to develop the best strategies for public health policies. public strategies include general isolation through quarantine and massive testing for focused isolation, with varying degrees of success so far, as can be analysed from the limited data available [5] . in this regard, mathematical modelling is an interesting approach that can allow the evaluation of different scenarios, furnishing information for a proper support for health system decisions. in general, nonlinear dynamics of biological and biomedical systems is the objective of several researches that can be based on mathematical modelling or time series analysis [6] . literature presents some examples related to the dynamics of infectious diseases. mathematical equations are widely used to model the nature and impact of global pandemics in the society. in particular, coronavirus propagation can be described by a mathematical model that allows the nonlinear dynamics analysis, representing different populations related to the phenomenon [7] . recently, the classical susceptible-infectious-recovered (sir) model proposed in [8, 9] , was employed in the analysis of the epidemic outbreak in different countries, including china, south korea, germany, italy, and france [10, 11, 12] . the modelling and evaluating the consequences of public health interventions. it was a direct application of previous developments [13, 14] on the fundamental problem of parameter identification in mathematical epidemic models, accounting for unreported cases. in this work the siru-type model is implemented for the direct problem formulation of the covid-19 epidemic evolution in brazil, adding a time variable parametrization for the fraction of asymptomatic infectious that become reported symptomatic individuals. according cotta et al. [5] it is an especially important parameter in the public health measure associated with massive testing and consequent focused isolation. the same analytical identification procedure is maintained for the required initial conditions, as obtained from the early stage exponential behaviour. however, a bayesian inference approach is here adopted for parametric estimation, employing the combined parameter and state estimation algorithm proposed by liu and wes and particle swarm optimization (pso). in this section, we formulate the mathematical sir model [5, 9, 10, 11, 12, 13, 14] we analyze is the following: at time t, let s(t) be the number of susceptible, i(t) the number of infected, r(t) the number of removed and permanently immune, u(t) and number of unreported symptomatic infectious individuals. the equations for the sir model 3 . 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 certified by peer review) the copyright holder for this preprint this version posted may 29, 2020. . https://doi.org/10.1101/2020.05.27.20115212 doi: medrxiv preprint where, where t 0 is the beginning date of the epidemic in days. asymptomatic infectious individuals i(t) are infectious for an average period of 1/ν days. reported symptomatic individuals r(t) are infectious for an average period of 1/η days, as are unreported symptomatic individuals u(t). according to cotta et al. [5] assumed that reported symptomatic infectious individuals r(t) are reported and isolated immediately, and cause no further infections. the asymptomatic individuals i(t) can also be viewed as having a low-level symptomatic state. all infections are acquired from either i(t) or u(t) individuals. the fraction f (t) of asymptomatic infectious become reported symptomatic infectious, and the fraction 1 − f (t) become unreported symptomatic infectious. the rate asymptomatic infectious become reported symptomatic is ν 1 (t) = f (t)ν, the rate asymptomatic infectious become unreported symptomatic is the transmission rate, τ(t), is also allowed to be a time variable function along the evolution process. figure 2 below illustrates the infection process as a flow chart [10] . the time variable coefficients, τ(t) and f (t), are chosen to be expressed as: these parameterized functions are particularly useful in interpreting the effects of public health interventions. for instance, the transmission rate, τ(t), is particularly affected by a reduced circulation achieved through a general isolation or quarantine measure, while the fraction f (t) of asymptomatic infectious that become reported, thus isolated, cases can be drastically increased by a massive testing measure with focused isolation. in the above relations, µ is the attenuation factor for the transmission rate, n is the time in days for application of the public health intervention to change transmission rate, µ f is the argument of the f (t) variation between the limits ( f 0 , f max ) e first time variable function has been previously considered, while the second one has been introduced in the present work, so as to allow for the examination of combined measures. the cumulative number of reported cases at time t, cr(t), which is the quantity offered by the actual available data, and the a priori unknown cumulative number of unreported cases, cu(t), are given by: the daily number of reported cases from the model, dr(t), can be obtained by computing the solution of the following equation and with initial conditions: . 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 certified by peer review) the estimation problem, also known inverse problems, is an interdisciplinary task involving experimental observations and numerical analysis in many fields of science and engineering. specifically in epidemiological studies, a crucial step is the determination of the extension of diseases. in this regard, the effort is made to infer the values of unknown states and parameters characterizing the system under investigation. the results of such studies can support developing public health policy. here, using the available data of infected individuals in brazil, we aim at solving a joint estimation of states and parameters (namely τ 0 , f 0 and µ for the siru model) in order to assess the covid-19 spread and, hence, to be able to predict locally the future progression of the pandemic. the estimation problem, also known as non-stationary inverse problems usually requires a system dynamic model, which provides the temporal evolution of the states and parameters, an observation model, which transforms the system variables to give the observed variables, and a estimation technique that relates the all available information to the process knowledge to obtain the desired estimate [15] . here, x x x represents the state vector, θ θ θ is the parameter vector, y y y is the vector of the observed variables, ε ε ε and δ δ δ are respectively the system and observation noise vectors. the function f f f indicates the evolution model and the function g g g is a observation model, both of them are nonlinear function of state variables and parameters. it is assumed that the noise vectors have zero mean and follow a normal distribution. the subscript k denotes the instant of time. there are many numerical methods that can approach the state and parameter estimation. however, as the model considered here is nonlinear and there may be high correlation between model parameters, local optimization methods such as gradient and direct search algorithms are not suitable since they strongly depend on the initial conditions. it is necessary to resort to the use of global methods capable of handling nonlinear systems, such as: 1. heuristic methods, including the particle swarm optimization (pso) technique which usually presents better performance than other heuristic algorithms [16, 17] ; and 2. sequential monte carlo methods, as the particle filter (pf) algorithms which makes use of random samples for a bayesian statistical inference. such methods do not suffer from instability as they do not solve the inverse problem as an optimization problem, but as a search or sampling problem [18] . in both classes of methods, a set of particles is used to find the solution for the estimation problem, i.e filtering the available data and estimating the parameter values that minimize the objective function, f ob j , which represents the model performance for the problem. in this work, we solve the estimation problem for the siru model considering the measurements as the cumulative number of reported cases (cr(t)) from brazil, using pso and pf algorithms presented below. before carrying on the estimation problem, useful information can be obtained if the onset of the pandemic is modelled as an exponential growth, as represented by the following equation 6 . 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 this version posted may 29, 2020. . https://doi.org/10.1101/2020.05.27.20115212 doi: medrxiv preprint after determining χ 1 , χ 2 and χ 3 , it is possible to explicitly calculate the unknown initial conditions for the model variables, estimates for the initial time of the pandemics and for the initial transmission rate [10, 9] : this technique was proposed by kennedy and eberhart [17] and improved by other researchers to assure the convergence to the global optimal solution. it considers that each individual of the swarm, called particle, representing a potential solution moves around in the multidimensional search space. balancing individuality and sociability of the particles, in order to locate the optimal solution, pso mimics the social behavior of various species adjusting dynamically the position (ξ k j ) and velocity (v k j ) for each particle j = 1, ..., m at each iteration k, in accordance with the following equations: in this formulation, j denotes the particle, k represents the iteration number, v is the velocity and ξ is the position of the particle. regarding the regions of the search space where the objective function f ob j (ξ j ) shows optimum values, b j is the best value found by the particle itself and b g is the best value found by the entire swarm. the coefficients r p and r g are uniform random numbers between 0 and 1; 0 < ω < 1 is related to inertial weight ; and finally φ p and φ g denote respectively individual cognition and the social parameters that must be chosen. a general description of the pso algorithm follows [17, 16] : 1: for each j = 1, · · · , m, set the initial conditions for the swarm: the position (ξ 0 j ) and velocity (v 0 j ) are randomly generated, given suitable ranges for the variables. 2: evaluate the objective function for each particle of the swarm, f ob j (ξ j ), and update eventually the best value found by the particle itself, b p , and the best value found by the entire swarm, b g . 3: update of the velocity of each particle of the swarm, v k+1 j . 4: update of the position of each particle of the swarm, in order to obtain the new position, ξ k+1 j . 5: check the stopping criteria; if it is not verified, return to step (2) for the next iteration. 7 . 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 this version posted may 29, 2020. . https://doi.org/10.1101/2020.05.27.20115212 doi: medrxiv preprint the estimation problem with pf methods is tackled in the form of a stochastic process, in which a set particles (or samples) with associated weights is to approximate the posterior density of the states and parameters. within the bayesian framework, all available information (measurements and phenomena involved) is used as a source of knowledge to determine the unknown variables. the prior distribution provides the necessary information to draw the first set of particles, which are updated through the evolution model and transformed by the observation model to give the estimates. the likelihood function is then used to compare such estimates with the experimental measurements, and incorporates more information, via particle weights, in order to determine the posterior distribution. sequentially, all new information is combined with the previous information to create the basis for the statistical procedure. such steps describe briefly the sequential importance sampling (sis) filter [19, 15, 20, 21] . the performance of the sis filter may be negatively affected by the degeneracy phenomenon, in which few particles contribute to the approximation of the posterior probability distribution [19, 20] . in this regard, the sampling importance resampling (sir) and auxiliary sampling importance resampling (asir) filters consider a resampling step to deal with the elimination of particles originally with low weights and the replication of particles with high weights, at each instant t k or whenever the number of effective particles falls below a certain threshold [22, 23, 24, 25, 26] . however, such filters are used to obtain estimates of state variables [19, 20] . in this work, we are particularly interested in the joint estimation of parameters and state variables, since estimating the parameters that regulate the dynamics of growth in the number of infected individuals is also very important to understand the phenomenon. for this purpose, we used the algorithm proposed by liu and west [27] . this algorithm is a generalization of the asir filter, and the inference is made on the joint posterior density π(x x x k , θ θ θ |d d d k ),where θ θ θ is the vector of parameters, d d d k contains the measurements up to time k and x x x k the state variables. time evolves to k + 1, we observe y y y k+1 and now want to generate a sample from p(x x x k+1 , θ θ θ |d d d k+1 ). bayes' theorem gives this as the filter is based on the hypothesis of [28] , which assumes that, for a vector of static parameters θ θ θ , the posterior density estimation p(θ θ θ |d d d k ) is done by smoothed density via kernel, [27] where t denotes the transpose of the matrix,θ θ θ is the mean of the posterior particles. in addition, a is related to a discount factor δ as follows, [27] a = 3δ − 1 2δ (17) where 0.95 < δ < 0.99 the general particle filter algorithm for combined estimation of parameters and state variables in time step k − 1, based on the measurements available in time k is given below, [27] 4 numerical results and discussion in all simulations presented here, we assumed the estimates 1/ν = 6.20798 and 1/η = 11.2784 days [5] for the average times in the model, and also set s 0 = 210.15 · 10 6 as the total of susceptible individuals in brazil. firstly, we used the data points related to the first month of the cumulative cases in brazil, from february, 26 2020 up to march 25, 2020 (30 days), to fit the early exponential growth. in the sequence, we estimated the model parameters via inverse problem analysis applying data from february 26, 2020 up to may 21, 2020 (85 days). besides that, we also considered that isolation measures were taken from march 17, 2020, when domestic isolation, remote work and shutting down temporarily businesses and services were recommended. the data points recorded from may 8, 2020 until may 21, 2020 (14 days), were used to verify the predictive capability of the proposed approach. this way, we used about 84% of the data set to estimate the siru model parameters (learning step) and 16% for validation, changing the estimated values, if necessary, of f 0 or µ to improve the model performance (prediction step). such computational studies for direct and inverse problems were performed in python on a computer with intel core i5 processor and 8 gb ram. the adjustment for the early growth of the cumulative infectious cases in brazil is displayed in figure 3 . we can see a satisfactory agreement between the data and the model, making clear that this phase of the pandemic is purely exponential. the estimated parameters for the model χ 1 = 4.185, χ 2 = 0.231, and χ 3 = 1.0. such result allowed obtaining an initial time for the growth 9 . 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. µ µ µ j k+1 = e x x x k+1 |x x x j k , θ θ θ j k may be computed from the state evolution density and m m m j k = aθ θ θ j k + (1 − a)θ θ θ k is the j th kernel location. 2: sample an auxiliary integer variable from the set {1, · · · , n} with probabilities proportional to g j k+1 ∝ w j k p y y y k+1 |µ µ µ j k+1 , m m m j k ; call the sampled index z. with weights w z k+1 , as required. . 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 this version posted may 29, 2020. at t 0 = −6.203. according to this model, a negative value for t 0 means that the starting time of the epidemic in brazil took place about six days before the first reported case, what may have happened on february 20, 2020. although such modelling cannot represent subsequent cases, we can use its parameters to find the remaining initial conditions, i 0 , u 0 and τ 0 , which have to be recalculated from within both pso and pf algorithms. to solve the estimation problem through the pso technique, we applied a time weighted cost function as the objective function f ob j = t · (cr meas − cr model ) 2 dt, where cr meas and cr model are the values of the measured and estimated cumulative cases at time t. we used 100 particles and 50 independent calls of the code. to tune the algorithm, we set the parameters ω = 0.9 and φ p = φ g = 2.0 [16] . firstly, to monitor the number of reported and unreported cases and infectious cases, we used the full data set (85 days) for estimation of the siru model parameters, f 0 , µ and τ(t) = g(t, τ 0 , µ). the adjustment with pso simulations led to the parameters f 0 = 0.39123, µ = 0.0109 and τ 0 = 1.426 · 10 −9 . in figure 4 , it is possible to note an excellent agreement of the simulated values with the measured values of the cumulative reported cases (figure 4-a) . however, the number of reported cases is not represented accurately, what can also be better observed in the figure 4 -b for the daily cases. in addition, the low value of the fraction f 0 indicates that about 40% of asymptomatic individuals became reported symptomatic infectious, meaning that a vast majority of the asymptomatic population was not diagnosed. however, the significant under reporting of cases 11 . 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 this version posted may 29, 2020. . are caused by low number of tests being carried out, delay in the official processing of information and more seriously the lack of test kits. such reasons make it difficult to fight covid-19 in brazil. the result for the number of asymptomatic and symptomatic infectious cases given by the model states, i(t), r(t) and u(t), which are not measured variables, is also obtained ( figure 5 ). infections may be transmitted from either asymptomatic individuals or unreported symptomatic individuals, which sum up more than 350,000 at this stage (may, 21 2020) of the pandemic in the country. it is known that most healthy people are likely to experience asymptomatic or mild cases; however, this fact makes the coronavirus spread control even harder. finally, in order to verify the predictive capability of this approach, we divided the problem into the learning and prediction steps as explained above. the best result of the simulations provided f 0 = 0.39123, µ = 0.0109 and τ 0 = 1.426 · 10 −9 . in figure 6 , from may 8, 2020, the prediction for 14 days is compared to the measured (or observed) values of the reported cases. we can see again that the siru model can be adjusted to represent the brazil data set, since there is an excellent agreement with the data used in the learning step. however, the prediction step shows a poor performance when one desires to use the estimated parameters in the learning step. this is probably because any pandemics is a dynamic process depending on many factors, such as individual behaviour against isolation enforcement, application rate of test kits and processing of information. since we used a pso algorithm that does not consider time-varying parameters and uncertainties, this approach failed to exhibit a different trend which was not present in the training data. 12 . 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 this version posted may 29, 2020. 13 . 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 this version posted may 29, 2020. . the development of a reliable forecasting model is fundamental to allow public policies to be adopted in advance, in order to avoid further increasing the number of infected individuals. so, proposing a different scenario to predict properly may be interesting to show that the siru model can represent this pandemic. in this sense, we consider that the most uncertain parameter of the model would be the attenuation factor µ, which depends on the quarantine and isolation measures to decrease the infection rate. keeping f 0 constant at the estimated value, we checked for different changes on µ to find a scenario in which the performance of the prediction phase step could be improved. according to the result in figure 6 , we found that reducing substantially the attenuation factor by 70% would suffice to improve the prediction for the reported cases. such result highlights the importance of considering state and parameter uncertainties. in this regard, we expect that the particle filter allows reaching a better prediction performance, what would make forecast analysis more reliable (or, at least, provide better understanding of the dynamic behaviour of the parameters)or, at least, understanding the time variation and range of the parameters. anyway, the best result of the pso algorithm is used merely here for comparison with the pf simulations, and to provide an initial estimate of the model parameters. we used the algorithm of liu & west for the particle filter technique in the estimation problem. such algorithm is suitable for the joint estimation of state variables and model parameters. the number of particles n part was set arbitrarily to 5000 and the results from the pso simulations were considered as initial guesses for the parameters. gaussian prior probability densities were assumed for the parameters f 0 and µ with standard deviations corresponding to approximately 1% of the means of each parameter. for the effect of the model uncertainty, we tuned throughout the simulations 0.001% for the number of individuals susceptible to infection, s(t), and 5% for the remaining states, i(t), r(t) and u(t) -such percentage is related to the previous value of the respective state. besides that, the uncertainty level for the observed cumulative cases, cr(t), changes over time. it started at σ cr = 30% in relation to the measured value and, as of march 17, 2020 when isolation was enforced, it was decreased in the simulation by a step-change to σ cr = 3%. to present the results, we calculated the estimation error, rmse = ∑ k (cr meas (k) −cr model (k)) 2 /σ 2 cr (k), and 95% credibility level for each state variable and parameter was calculated as the 2.5% and 97.5% quantiles . the posterior distributions of each state and parameters estimated on may 07, 2020 (last day of the learning step) provided the respective initial condition for the prediction step. lastly, we also performed an additional step to forecast new covid-19 cases during 120 days (from may 22, 2020 to september 17, 2020). in the prediction and forecast horizons, the model parameters are updated via random walk model. using the full data set (february 26, 2020 to may 21, 2020), the estimation with the algorithm of liu & west significantly improved the agreement of the simulated values with the measured values (figure 7) , especially for those measured points near the end of the considered period. this was possible due to the dynamic estimation of the parameters (figure 8 a and b) , which were varied over time from the initial guess. the attenuation factor was increased about 30% from the initial guess, showing that isolation has been effective at some extent decreasing the transmission rate, . 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 this version posted may 29, 2020. . τ(t). the fraction of report shows that over 60% of symptomatic infectious cases were not reported in this period. the improvement obtained in comparison to the pso result can be seen from the estimation error rmse (figure 8d) , which was consistently decreased. regarding the infectious cases, the estimation is alarming since the group of potential transmitters is increasing (figure 9 ). the number of the infectious population that may not have been diagnosed (that is, asymptomatic and unreported symptomatic individuals) is estimated to be more than 450,000 cases. hence, it is worthy to point out that massive, rapid tests and restrictive measures are paramount to curb the spread of the virus. (a) 26 the capability of the model to predict was analyzed using the available data of reported cases in brazil from february 26, 2020 up to may 7, 2020. according to figure 10 , the adjustment of the parameters found in the learning step is suitable to predict accurately the pandemic evolution up to may 18, 2020 (10 days ahead), which would have presented in advance the notification of more than 115,000 cases. from this result, we simulated the model considering 120 days from may 21, 2020 to forecast new cases. the dynamic behaviour of the parameters in both steps can be seen in figure 11 . the forecasted values for the daily reported cases and for the infectious cases are shown in figures 12 and 13 , in which we highlighted each analysis step (estimation, prediction and forecast). the result suggests that the epidemic peak in brazil are due to be reached around mid-june, 2020, 15 . 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 this version posted may 29, 2020. 16 . 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 this version posted may 29, 2020. with almost 25,000 cases being notified a day. specifically, it can inferred that the number of asymptomatic individuals may increase up to 400,000 cases and, more importantly, the number of unreported symptomatic cases around 460,000 may be twice greater than the number of reported symptomatic. in brief, this means that number of people requiring medical assistance will increase dramatically in the future. according to the forecast, the pandemics in brazil is expected to slow down beyond the peak of daily number of cases and the number of cumulative reported cases to be more than 1,500,000 ( figure 14) . so, if such numbers impose a burden on the health system, it is important to enhance isolation measures, as quarantine and social distancing. as brazil is a very large country, the spread of the virus is supposed to vary from region to region, such way that community containment measures may be established locally at different moments. . 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 this version posted may 29, 2020. 18 . 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 certified by peer review) the copyright holder for this preprint this version posted may 29, 2020. . 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 certified by peer review) the copyright holder for this preprint this version posted may 29, 2020. . https://doi.org/10.1101/2020.05. 27.20115212 doi: medrxiv preprint since the coronavirus outbreak has been evolving rapidly, this work considered a numerical application to predict the evolution of a covid-19 epidemic in brazil. we implemented the model siru to represent the coronavirus spread and used the cumulative reported cases as measurement. for the estimation problem, an inverse problem was solved under the bayesian framework with particle filter. specifically, we used the algorithm of liu & west to perform a joint estimation of states and parameters. besides that, particle swarm optimization based simulations provided initial guesses for this problem. the model was calibrated to represent the number of reported cases and validated using two-week real data. afterwards, we performed a forecast step to predict new cases of the disease. it was found that the pandemic peak is expected to take place in mid-june, 2020 with about 25,000 news cases a day and over 1,500,000 individual will have tested positive for covid-19 up to september, 2020. such result reinforces the need for social distancing measures and for diagnostic tests to decrease the transmission rate and the number of infected people in severe condition. . 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 certified by peer review) the copyright holder for this preprint this version posted may 29, 2020. . https://doi.org/10.1101/2020.05.27.20115212 doi: medrxiv preprint a pneumonia outbreak associated with a new coronavirus of probable bat origin abnormal respiratory patterns classifier may contribute to large-scale screening of people infected with covid-19 in an accurate and unobtrusive manner brazil is projected to be the next global covid-19 pandemic epicenter parametric identification and public health measures influence on the covid-19 epidemic evolution in brazil chaos and order in biomedical rhythms", journal of the brazilian society of mechanical sciences and engineering infectious diseases of humans understanding unreported cases in the covid-19 epidemic outbreak in wuhan, china, and the importance of major public health interventions predicting the cumulative number of cases for the covid-19 epidemic in china from early data. medrxiv predicting the number of reported and unreported cases for the covid-19 epidemic in south korea, italy, france and germany a covid-19 epidemic model with latency period. infectious disease modelling the parameter identification problem for sir epidemic models: identifying unreported cases identifying the number of unreported cases in sir epidemic models. mathematical medicine and biology : a journal of the ima statistical and computational inverse problems nonlinear parameter estimation through particle swarm optimization particle swarm optimization particle swarm optimization and uncertainty assessment in inverse problems a tutorial on particle filters for online non-linear/non-gaussian bayesian tracking beyond the kalman filter novel approach to nonlinear and non-gaussian bayesian state estimation. institution of electrical engineers application of particle filters to regional-scale wildfire spread particle filter-based monitoring scheme for simulated bio-ethylene production process propylene polymerization reactor control and estimation using a particle filter and neural network sequential state inference of engineering systems through the particle move-reweighting algorithm combined parameter and state estimation in simulation-based filtering approximating posterior distributions by mixtures key: cord-316993-mv577rok authors: marra, v.; quartin, m. title: an estimate of the covid-19 infection fatality rate in brazil based on a seroprevalence survey date: 2020-08-21 journal: nan doi: 10.1101/2020.08.18.20177626 sha: doc_id: 316993 cord_uid: mv577rok we infer the infection fatality rate (ifr) of sars-cov-2 in brazil by combining three datasets. we compute the prevalence via the population-based seroprevalence survey epicovid19-br, which tested 89000 people in 3 stages over a period of 5 weeks. this randomized survey selected people of 133 cities (accounting for 35.5% of the brazilian population) and tested them for igm/igg antibodies making use of a rapid test. we estimate the time delay between the development of antibodies and subsequent fatality using the public sivep-gripe dataset. the number of fatalities is obtained using the public painel coronavirus dataset. the ifr is computed for each survey stage and 27 federal states. we infer a country-wide average ifr of 1.05% (95% ci: 0.96-1.17%) and find evidence for its increase starting in june 2020. the infection fatality rate (ifr) is one of the most important quantities of any new disease. an accurate estimate of both the case fatality rate (cfr) and ifr is thus usually a challenge before the end of a pandemic. 1 it is, nevertheless, a very important endeavor as it has direct implications on the amount of resources and effort that should be allocated to prevent the spread of the disease and help steer policy-making in general. for instance using the united states as reference, perlroth et al. 2 concluded that a cfr below 1% makes schoolclosures and social distancing not cost-effective. in order to estimate the ifr one needs not only an estimate of the number of deaths, but also of the total infected population, and then to compare both within the same time period. it is, therefore, a difficult task as many cases are asymptomatic or develop only mild symptoms and are often unaccounted for. it is also hampered due to the lack of testing in many countries. 3 the total number of deaths during an epidemic can be biased by the mislabeling of undiagnosed fatalities. to circumvent this possibility, one can rely on statistical estimates from the study of the excess deaths in a given period of time. in the case of covid-19 this method is being pursued by many groups, 4-6 including the mainstream media, 7-9 as a method which is complementary to the officially reported numbers. however, this approach invariably suffers from important modeling uncertainties. 5 this may be especially true during the current pandemic which has seen an unprecedented amount of disruption of economic activity and social behavior, which includes a large fraction of the population undertaking social distancing measures. 10 one of the first detailed analysis of the ifr of covid-19 was based on around 70 thousand clinically diagnosed cases in china. after adjusting for demography and under-ascertainment verity et 15 on the other hand, a report by the group at imperial college london estimated much higher values for the 16 brazilian states they considered, 16 which, combined, suggest an overall ifr of 0.9%. the incompatible estimates above highlight the 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 certified by peer review) the copyright holder for this preprint this version posted august 21, 2020. herent uncertainty in modeling a new disease that has caused such an unprecedented change in lifestyle worldwide. this is the main reason why one should rely on seroprevalence estimates in order to estimate the ifr of covid-19. in a recent study, relying on antibody screening of blood donors, the ifr was estimated to be much lower, less than 0.21% at 95% cl. 17 such an approach is, however, limited by the fact that blood donors may not be representative of the population. in particular all donors are younger than 70 and healthy. the ideal approach to circumvent the limitations above is to conduct random serology studies in the population. one such study -conducted in geneva, switzerland, with 2766 participants -found that for every reported covid-19 case there were another 10.6 unreported ones, 18 a large discrepancy which again stresses the difficulties that models have to deal with. the same group reported an ifr of 0.64% (95% ci: 0.38-0.98%). 19 a much larger survey with 61075 participants was conducted in spain, but ifr estimates were not reported. 20 a meta-analysis of 36 seroprevalence studies performed by ioannidis 21 found that the ifr values ranged from 0.00% to 1.31%, and among 32 different locations the median ifr was 0.24%. another meta-analysis of 25 ifr studies found an ifr of 0.68% (95% ci: 0.53-0.82%). 22 these results hint at a possible large variation in ifr values around the globe, although data from different countries were reported to be highly heterogeneous. in brazil, a large random seroprevalence study was performed by the epicovid19-br team 23 which aimed to test 250 individuals in each of the 133 selected large sentinel cities. it has so far been carried out in 3 stages using the wondfo lateral flow test for immunoglobulin m and g antibodies against sars-cov-2. the first stage was conducted between may 14 and 21, 2020, but did not reach its target number of samples, and in only 90 of the 133 cities at least 200 tests were performed. the total number of tests in all cities was 25025. round 2 was conducted from june 4 to 7 and reached over 200 tests in 120 cities. considering all cities a total of 31165 individuals were tested. round 3 was performed between june 21 and 24 and made over 200 tests in all 133 cities for a total of 33207 tests. the total number of tests in all rounds was 89397, see figure 1 . the covid-19 pandemic has strongly affected brazil. 24 the federal government response has been heavily criticized, 25 and in august 2020 the number of confirmed cases and deaths crossed 3 million and 100 thousand, respectively, second only to the usa in raw numbers. furthermore, strong ethnic end regional variations in hospital mortality were found, casting doubts on the availability of public health care for the sections of society that cannot afford private care. 26 this daring situation motivates even further the need for an estimation of the ifr which is as accurate as possible in order to trigger an adequate political response to the crisis. as summarized by figure 1 , in order to estimate the ifr we make use of three complementary datasets. we compute the percentage p a (t) of brazilians that have been infected by sars-cov-2 at the city, state and brazilian levels via the epicovid19-br data. we robustly correct for false positive and negative rates and combine prevalences from different cities without neglecting the non-gaussian nature of the distributions (details in the supplementary materials). the result is shown in figure 2 and in table i (the federal state acronyms explanation and full numerical tables can be found in the supplementary materials). we note a sharp increase in prevalence between rounds 1 and 2, and a subsequent stabilization between rounds 2 and 3. the state of pará (pa) exhibits an unexpected sharp decrease in prevalence in the last round, possibly due to a heterogeneity in the sampled population. we obtain the number of fatalities via the public painel coronavírus dataset. 27 painel coronavírus is the brazilian reference to keep track of the pandemic at the federal level and provides the deaths by covid-19 with their geographic location. we cannot compute the ifr directly via the ratio of p d and p a because, at a given timet, there are patients that developed antibodies but did not die yet from the disease. 28 in order to estimate the time delay τ ad between the development of antibodies and subsequent fatality we use the public sivep-gripe dataset ("sistema de informação da vigilância epidemiológica da gripe"), . 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 this version posted august 21, 2020. . https://doi.org/10.1101/2020.08.18.20177626 doi: medrxiv preprint a prospectively collected respiratory infection registry data that is maintained by the ministry of health for the purposes of recording cases of severe acute respiratory syndrome (sars) across both public and private hospitals. the sivep-gripe dataset contains the dates of symptoms onset and death for patients with sars-cov-2 positive rt-pcr test, together with their geographic location, which allow us to estimate the time delay τ sd between the development of symptoms and subsequent fatality. we also make use of an empirical distribution between the first symptoms and the development of antibodies 29 to estimate the mean time-delay τ sa between both events. together, these estimates allow us to obtain the time-delay τ ad τ sd − τ sa . for the whole brazil we find τ ad 10.3 days. table ii summarize all the estimated time-delays which are used in our calculations (details in the supplementary materials). using this combined information we can then compute the ifr at the state and country levels: wheret is the time of a given epicovid19-br phase. the results for brazil are given in table i and figure 3 , the ones for the states (combining all rounds) in figure 4 . we see in figure 3 that round 3 exhibits a considerably higher ifr, which we explore below. we note significant statistical tensions in the data of two states: pará (pa) and roraima (rr). we therefore consider their ifr estimates unreliable, but due to their small population they have insignificant impact on the ifr estimates at the country-level. the numerical results for all the states and for the three rounds separately can be found in the supplementary materials. the confidence interval was computed by combining the statistical sources of error and including the non-gaussian nature of the distributions. our overall estimate of the ifr of 1.05% (95% ci: 0.96-1.17%) is in agreement with some, but not all, of the previous world estimates discussed earlier. in particular, at the country level, our combined estimate agrees qualitatively with the one by the imperial college covid-19 response team, 16 even though their result falls outside our 95% ci. at the state level we also find some disagreement between their values and our 95% cis, see figure 4 . our estimate is also very precise: the statistical error is smaller than the aforementioned similar studies. however, it may suffer from a number of systematic biases related to each of the three datasets, which we now discuss. first, we are assuming that sars-cov-2 antibodies remain present in the patients. indeed, there are reports that igg levels fade in recovered patients on a timescale of a few months. 30 even if confirmed, this effect should have only a small impact on our results since the last round of epicovid19-br was performed on 22/jun/2020, still early in the brazilian epidemic progression. in fact, the number of confirmed cases in brazil had increased over 20-fold in the preceding 2 months, which means that our ifr estimates must be dominated by recent infections. in any case, the fading of igg levels leads to an underestimate of p a and an overestimate of the ifr. one may speculate that the observed increase in ifr in round 3 may be a result of fading antibody levels-antibodies prevalences are indeed cumulative. we checked this hypothesis and found that the higher ifr of round 3 persists if we limit the number of deaths between the delayed timet + τ ad and 90 days earlier, which is equivalent to assume a sharp drop of igg levels after such a time period. consequently, we rule out this explanation and rather propose that the higher ifr is due to hospital bed saturation in june and july. 31 this may be particularly relevant in the context of the public health care, which serves 75% of the population but its total spending is similar to the that of the private health care, implying that, on average, a patient in a private hospital costs three times more than one in a public hospital. 32 second, not all covid-19 related deaths may be registered in painel coronavírus. one expects this to happen for out-of-hospital fatalities and be stronger in the poorest areas with a less present health care infrastruc-. 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 this version posted august 21, 2020. figure 4 . combined ifr using all 3 rounds (maximum likelihood and 95%ci). the black dots represent model-based results by the imperial college covid-19 response team. 16 the horizontal red line is the ifr estimate for brazil given in table i . two states have unreliable combined ifr results and are shown in light gray: pa has a significant decrease in pa in round 3 that cannot be a simple fluctuation; rr has a very low ifr in round 2 which is in tension with the other rounds and artificially shrinks the ci. ture. as we are analyzing the 133 large sentinel cities that entered the epicovid19-br survey this bias is not expected to be sizable. its effect is, nonetheless, the underestimation of the ifr. a third potential bias comes from the fact that the time in painel coronavírus is not the actual time of death but rather the time of notification. in order to alleviate this issue and also average out oscillations due to weekends, we smooth the dn d /dt data according to a forward 7-day moving average (details in the supplementary materials). finally, the sivep-gripe dataset is biased towards cases with severe symptoms. indeed, there is a significant number of cases that are hospitalized when symptoms are notified (see supplementary materials). we took this into account via a delay parameter τ ∆ = τ sd − τ sivep sd = 2 ± 1 days (see table ii ) which models the time that a patient takes to go from symptoms onset to severe symptoms (details in the supplementary materials). had we set τ ∆ = 0, we would have obtained for the ifr in brazil a value of 1.02% (95% ci: 0.93-1.13%), a 3% lower estimate. it is important to stress that the overall ifr we computed is relative to the 133 large cities that were tested by the epicovid19-br survey. these cities amount to 35.5% of the brazilian population and one may speculate that the ifr may be different in smaller cities and rural or poorer areas. as new medications and treatment protocols for the disease are discovered and become available it is hoped that the ifr will decrease. since our data comes from the first months of the pandemic, our results therefore also set a baseline for future comparisons of the fight against covid-19 in brazil. concluding, we hope that our careful evaluation of the ifr in brazil will help reinforce, at the federal, state and municipal levels, the seriousness of the covid-19 pandemic and the urgency of taking the proper actions in order to reduce its societal and economic impact. health outcomes and costs of community mitigation strategies for an influenza pandemic in the united states coronavirus (covid-19) testing pandemic in the united states excess deaths from covid-19 and other causes excess mortality during the covid-19 pandemic: early evidence from england and wales a pandemic primer on excess mortality statistics and their comparability across countries tracking covid-19 excess deaths across countries tracking covid-19 excess deaths across countries impactos econômicos da covid-19 estimates of the severity of coronavirus disease 2019: a model-based analysis estimating clinical severity of covid-19 from the transmission dynamics in wuhan, china estimating the burden of sars-cov-2 in france using early data to estimate the actual infection fatality ratio from covid-19 in france brazilian modeling of covid-19 (bram-cod): a bayesian monte carlo approach for covid-19 spread in a limited data set context report 21: estimating covid-19 cases and reproduction number in brazil estimation of sars-cov-2 infection fatality rate by real-time antibody screening of blood donors seroprevalence of anti-sars-cov-2 igg antibodies in geneva, switzerland (serocov-pop): a population-based study serology-informed estimates of sars-cov-2 infection fatality risk in geneva, switzerland prevalence of sars-cov-2 in spain (ene-covid): a nationwide, population-based seroepidemiological study the infection fatality rate of covid-19 inferred from seroprevalence data a systematic review and meta-analysis of published research data on covid-19 infection-fatality rates remarkable variability in sars-cov-2 antibodies across brazilian regions: nationwide serological household survey in 27 states evolution and epidemic spread of sars-cov-2 in brazil covid-19 in brazil:"so what? ethnic and regional variations in hospital mortality from covid-19 in brazil: a cross-sectional observational study brazilian ministry of health real estimates of mortality following covid-19 infection antibody responses to sars-cov-2 in patients with covid-19 clinical and immunological assessment of asymptomatic sars-cov-2 infections ocupação de uti volta a subir e supera 80% em 13 capitais saúde pública: um panorama do brasil mq's research is partially supported by the brazilian research agencies cnpq and faperj. vm's research is partially supported by brazilian research agency cnpq. funding: this project has not received any funding. author contributions: both authors contributed equally for this work. competing interests: the authors declare no competing interests. data and materials availability: the wolfram mathematica codes and the data used for this work are available at: www.github.com/mquartin/covid19-ifr-br. key: cord-021377-1qac76tn authors: barstow, anita l.; leslie, david m. title: leopardus braccatus (carnivora: felidae) date: 2012-04-09 journal: nan doi: 10.1644/891.1 sha: doc_id: 21377 cord_uid: 1qac76tn leopardus braccatus (cope, 1889) is a small felid—not much larger than a domestic house cat—commonly called the pantanal cat. no comprehensive surveys have been conducted to determine how many l. braccatus exist in the wild. it is found in humid, warm grasslands and wooded areas of extreme northwestern argentina, southwestern and southand north-central (newly reported ranges) brazil, paraguay, and uruguay. habitat loss and degradation are considered major threats throughout most of its range. it is uncommon in captivity and museum collections, listed with all felidae under appendix ii of the convention on international trade in endangered species of wild fauna and flora, and considered “near threatened” by the international union for conservation of nature and natural resources in the pampas cat group ( = l. colocolo). context and content. order carnivora, suborder feliformia, family felidae; subfamily felinae. the relationships within this genus are controversial and currently in flux (see species' "context and content" for relationships as they pertain to this species). we have chosen to follow wozencraft (2005) , who listed 9 species (braeeatus, eoloeolo, geoffroyi, guigna, jacobitus, pajeros, pardalis, tigrinus, and wiedii) under leopardus. leopardus braccatus (cope, 1889) pantanal cat felis braeeata cope, 1889:144 . type locality "province of rio grande do sui, or in matto grosso," brazil; restricted to "chapada, matto grosso" by j. a. allen (1919b:378) . lynchailurus pajeros braeeatus: j. a. allen, 1919b:376. name combination. felis (mungofelis) braeeatus: antonius 1933:13 . name combination. lynehailurus eoloeolus braeeatus: cabrera 1940:12. name combination. felis eoloeola muiioai ximenez, 1961: 1. type locality "uruguay." leopardus braeeatus: wozencraft, 2005:537 . first use of current name combination. context and content. context as for genus. taxonomy of south american small felids has been in flux for at least the past several decades. they have been classified under various genera (e.g., felis, leopardus, lynehailurus, and oneifelis) and have been split into separate species (e.g., garcia-perea 1994; wozencraft 2005) , often monotypically, or lumped with various combinations of subspecies (e.g., sunquist 2002, 2009 ). relatively recent molecular evidence (cossios et al. 2007 (cossios et al. , 2009 johnson et al. 1996 johnson et al. , 2006 johnson and o'brien 1997; masuda et al. 1996; mattern and mclennan 2000; o'brien and johnson 2007; o'brien and yuhki 1999; pecon-slattery and o'brien 1998) suggests a phylogeny favoring various subspecific designations, in contrast to systematic conclusions based on just morphological characteristics that suggest unique species (garcia-perea 1994) . using morphological characteristics, garcia-perea (1994) assessed the taxonomy of some south american small felids, formerly grouped under felis eoloeolo, with 86 specimens from argentina, brazil, chile, ecuador, paraguay, peru, and uruguay, consisting of 72 study skins and 51 skulls, from 8 north american, south american, and european collections. she grouped them under lynehailurus into 3 species: braeeatus (with the 2 subspecies above; fig. 1 ), pajeros (7 subspecies), and eoloeolo (2 subspecies). the size of the ectotympanic bone relative to caudal entotympanic bone of leopardus is usually consistent within species, but some variation in the inflation of the posterior chamber may be seen among species (garcia-perea 1994) . two to 5 distinguishing characteristics of the skulls (e.g., bullar region, orbital region, palatal region, and neurocranium) and teeth were found among the various specimens of leopardus, designated collectively as "pampas cats" (garcia-perea 1994). small felids generally show a great deal of variation in coat patterns and colors. considering all metrics, as well as geographic affinities, garcia-perea (1994) classified 3 "types" of pampas cats and concluded that colocolo should be split into 3 species (braccatus, colocolo, and pajeros) with which wozencraft (2005) concurred. sunquist and sunquist (2009:146) formally considered braccatus to be 1 of 8 subspecies of l. colocolo, but they noted that "braccatus and pajeros likely represent distinct species." most recently, nascimento (2010) , in his unpublished dissertation, identified 16 species of leopardus based on 29 cranial measurements and 14additional morphological traits from 591 museum specimens; he elevated l. braccatus munoai to a full species. conservation of south american small cats may be the most significant and pressing reason to consider their populations unique enough for special recognition and action ). here, we followed wozencraft (2005), who listed 2 subspecies of braccatus: (cope, 1889) . see above. l. b. muiioai ximenez, 1961 . see above. nomenclatural notes. the etymology of leopardus braecatus is latin meaning lion-panther and wearing breeches. common names of l. braccatus include pantanal cat, gato palheiro (garcia-perea 1994), and bush cat (miller 1930 ). the ectotympanic bone of leopardus braccatus lacks significantposteroventral expansion or inflation and represents only 20-250/0 of the bullar volume, in contrast to the colocolo, l. colocolo (40-500/0), and the pampas cat, l. pajeros (25-350/0-garcia-perea 1994) . shape of the notch for the postpalatine vein in the palate is "narrow and deep" in l. braccatus and "wide and comparatively shallow" in l. colocolo and l. pajeros (garcia-perea 1994:11) . the frequency of the presence of p2 is higher in l. braccatus (630/0, n = 8) than in l. colocolo (330/0, n = 6) and l. pajeros (00/0, n = 21). shape of the main cusp (paracone) of l. braccatus is "short and wide in lateral aspect, lacking the sharp appearance" seen in l. colocolo and l. pajeros (garcia-perea 1994:15) . the anterior cusp (parastyle) of p3 tends to be absent in all felids except big cats (salles 1992); however, gracia-perea (1994)noted its presence in 3 specimens that she classified as l. braccatus and its absence in l. colocolo and l. pajeros. lingual tubercles on c1 occur with the highest frequency in l. braccatus and at very low frequency in l. pajeros; they are absent in l. colocolo (garcia-perea 1994). garcia-perea (1994) describes all species in the "pampas cat" group, including leopardus braccatus, as follows: face has 2 transverse brown to black lines that cross each cheek; superior line starts in the external comer of the eye; inferior line is almost parallel running up around the lateral side of the cheeks; and a 3rd line appears in some specimens at the dorsal end of the inferior line coming from under the chin and throat, creating a sharp angle where the 2 meet on the lateroposterior side of the cheeks. underside of the chin is white; throat is the same color as the basic coat color, or is somewhat lighter orangish brown, and has 2 or 3 brown stripes that originate on 1 side of the neck and run under the throat to the other side. there are reports of melanistic "pampas cats" in captivity, but a camera-trap photo in emas park, goias state, brazil, seems to be the only known record in the wild (silveira 2005) . there are 2 types of pelage in l. braccatus. the 1st type is "almost uniform brown agouti color dorsally" with traces of "dark brown rosettes on flanks" and is characteristic of l. b. braccatus (garcia-perea 1994:19 ; http://www.catsg.org/ catsgportal/project-0-month/02_webarchive/grafics/sept2005. pdf, accessed 18 january 2012). the spinal crest of l. b. braccatus is a little darker than the basic pelage; tail is not ringed but has 2 or 3 lines that do not completely circumvent the tail above a black tip. there are at least 2 (but can be as many as 4) heavy black stripes that wrap around the front legs, and similar stripes on the hind legs, although those stripes may not completely meet on the anterior part of the leg. spotted ventral markings of l. b. braccatus are black; throat is white, grading into orange behind the 1st throat stripe; feet are black dorsally and ventrally, including wrists and ankles, giving the distinctive appearance of wearing boots (allen 1919b; garcia-perea 1994; miller 1930; pocock 1941) . the 2nd pelage type, typical of l. b. munoai, has a background color that is paler and more yellow to orangish on the back and flanks (fig. 1 ). brown spots on flanks are more noticeable than in l. b. braccatus, and the feet are black only on palmar and plantar surfaces. the tail of both subspecies is variously tipped in black. in contrast to l. b. braccatus, the black tip of l. b. munoai is reduced, and the tail, itself has only a few discontinuous rings (garcia-perea 1994) . ears of leopardus are large and pointed rather than rounded as in other south american small felids (silveira 1995) ; they are usually black on the anterior one-half and gray on the rest of the surface (silveira 1995) ; and sometimes there is a pale spot toward the tip of the posterior surface of the ear. the hairs are longer on l. braccatus than on other south american species of leopardus. head-body length of leopardus, in general, is 423-750 mm; tail length is 220-330 mm; and mass is 2.9-3.7 kg (garcia-perea 1994; nowell and jackson 1996; redford and eisenberg 1992; silveria 1995; sunquist and sunquist 2002) . redford and eisenberg 1992; sunquist and sunquist 2009; ximenez 1961) . because of its extensive range, l. b. braccatus occurs in many more habitat types than l. b. munoai. a cat matching garcia-perea's (1994) description of l. b. braccatus was livetrapped in minas gerais, brazil, except the feet were only black on the palmar and plantar surfaces instead of having the characteristic boot pattern. the wild cats of brazil project, or projeto gatos de mato-brasil (de oliveira 2005 ; http:// www.wildcatconservation.org/wild-cats-of-brazil.html.accessed 26 september 2011) also found camera-trap evidence of l. b.braccatus from maranhao state of northern brazil; sanchez-soto (2007) recorded a road-killed specimen in mato grosso do sui, brazil; and chebez et al. (2008) documented its presence in argentina-all greatly expanding the known range of this subspecies (bagno et al. 2004; chebez et al. 2008; de oliveira 2006; garcia-perea 1994; sanchez-soto 2007; silveira 2005) . therefore, the approximate range of l. b. braccatus is between 2°s and 22°s and 45°w and 61°w (fig. 2) . l. b. munoai occurs only in uruguay and the state of rio grande do sui, brazil. its primary habitat is savanna that occurs from sea level to 514 m above mean sea level (bagno et al. 2004; chebez et al. 2008; de oliveira 2006; garcia-perea 1994) . a dorsal crest is distinctive of the pampas cat group, in which hairs are longer (7 em) than elsewhere on the body and flanks (1-3 cm-allen 1919b; nowell and jackson 1996) .the crest is about 3 em wide and runs from the back of the neck to the base of the tail; it is reduced in some specimens of l. braccatus, making it rather inconspicuous (courtenay 2002) . both (nonmelanistic) pelage types have 3 or 4 dark brown, almost black, stripes that circumvent the legs, but they may be incomplete on the inner side of the back legs. the formation of the panamanian land bridge permitted endemic small felids of north and central america to disperse extensively into south america (eizirik et al. 1998; johnson et al. 1996; johnson and o'brien 1997; o'brien and yuhki 1999; pecon-slattery et al. 1994; seidensticker and lumpkin 2004; wayne et al. 1989 ). the land bridge was completely established about 3 million years ago (coates and obando 1996) , but sea-level changes interrupted its formation several times until the mid-pleistocene (beu 2001) , suggesting that felid speciation also occurred in south america and recent diversity could be explained by a minimum of 5 or 6 immigrations (prevosti 2006) . nine of the 10 neotropical small felids are in a monophyletic group known as the ocelot lineage (collier and o'brien 1985; eizirik et al. 1998; mattern and mclennan 2000; pecon-slattery et al. 1994; salles 1992) . the fossil record of the ocelot lineage is very fragmentary, but specimens are known from the ensenadan age 2-0.5 million years ago (berta 1983; prevosti 2006) . "felis" vorohuensi from buenos aires province, argentina, was described by berta (1983) and considered plio-pleistocene in age. prevosti (2006) restricted the age of this fossil to 0.78-0.5 million years ago after reexamination of biostratigraphic and chronostratigraphic data from the locality. the oldest fossils of leopardus colocolo are from late ensenadan (0.78-0.5 million years ago) and bonaerianlujanian (0.5 million-8.5 thousand years ago) localities in the pampean region of argentina (prevosti 2006) . a fossil of l. colocolo also was found in tierra del fuego, chile, an island not currently inhabited by felids, and thought to be as young as the late pleistocene or early holocene (prevosti 2006) . l. colocolo split from, the common ocelot ancestor about 1.7 million years ago, based on molecular estimates . a fossilized left humerus identified as l. braccatus from the late pleistocene-early holocene recently was found in serra da bodoquena, mato grosso do sui, brazil, near the type locality (perini et al. 2009 ). leopardus braccatus has retractable claws that are large, compressed, sharp, and strongly curved (nowak 1991) and digitigrade adaptations of the feet (flynn et al. 1988) . except for the pads, hairs occur on the feet that allow it to silently stalk prey (nowak 1991). ears are large in relationship to head and forward facing, but they can be rotated slightly. eyes face forward with binocular vision for sharp visual acuity (flynn et al. 1988 ); pupils of the eyes adduct creating a vertical slit. the tongue is covered with sharp-pointed, backward-facing, calcified papillae (flynn et al. 1988 ) used for lacerating and retaining food within the mouth and for grooming. the skull is rounded and shortened anteriorly (fig. 3) . published skull measurements of l. braccatus are very limited, but in the 2 populations that garcia-perea (1994:table 4) classified as braccatus, ranges (mm) were: greatest length of skull, 94.3-100.5 (4 males); condylobasallength, 89.4-91.8 (4 males); rostral width across the canines, 21.6-24.1 (4 males); mastoidal width, 39.2-42.9 (4 males); interorbital width, 17.2-18.3 (4 males); postorbital width, 27.4-29.7 (3 males); zygomatic width, 62.1-67.5 (4 males and 1 female); length of p4 at the cingulum, 11-13 (4 males and 1 female); and mandibular length, 58.8-63.8 (4 males and 1 female). dentition reflects the highly predatory lifestyle of an obligate carnivore. the dental formula of l. braccatus is i 3/3, c 1/1, p 3/2, m 1/1, total 30 (garcia-perea 1994; nowak 1991). population characteristics.-there has been limited research on the ecology of leopardus braccatus, so aspects of its ecology and behavior are inferred here from reports on the "pampas cat" group in general (bagno et al. 2004; chebez et al. 2008; cossios et al. 2007 cossios et al. , 2009 eizirik et al. 1998; garcia-perea 1994; johnson and o'brien 1997; masuda et al. 1996; mattern and mclennan 2000; napolitanoet al. 2008; nowell and jackson 1996; o'brien and yuhki 1999; pecon-slattery et al. 1994 pecon-slattery and o'brien 1998; silveira 2005) . longevity ranges from an average of 9 years in the wild up to 16.5 years in captivity (nowell and jackson 1996) . litter size is 1-3 kittens, and a captive female 'gave birth at 24 months of age (nowell and jackson 1996; redford and eisenberg 1992) . gestation is 80-85 days (golden 2003) . space use.-home-range size of leopardus braccatus was 3.07-36.98 km 2 (sd = 23.33 krrr') in brazilian grasslands (silveira 2005) . individual pampas cats appeared to be diurnal with some crepuscular and only occasional nocturnal activity (cabrera and yepes 1960) . radiotracking studies by silveira (2005:4) found "virtually no activity during night time." vocalizations of l. braccatus are similar to other small felids and include meow, growl, spit, hiss, gurgle, and purr (sunquist and sunquist 2002) . leopardus braccatus is known to occur in many biomes in south america including the pantanal, chaco, pampas, cerrado, espinal, monte, deciduous forests, and transitional areas, all found in argentina, brazil, paraguay, and uruguay. these habitats are being rapidly converted from native vegetation to cattle ranching and agricultural fields, and severe fragmentation by roads and urban sprawl are growing problems throughout the range of l. braccatus (bagno et al. 2004; cavalcanti and gese 2009; soisalo and cavalcanti 2006; trolle 2003) . l. braccatus is reportedly found in pastures and agricultural fields, demonstrating that it can use human-altered habitats (bagno et al. 2004 ) and adapt to changing environments. within the range of l. b. munoai in uruguay and southern brazil, the paraguay and rio de la plata river basins are believed to be barriers to dispersal and gene flow . leopardus braccatus occupies humid and warm grasslands and forests from sea level to 2,000 m (garcia-perea 1994; . annual rainfall varies within the range of l. braccatus because it occurs in a wide variety of ecotypes: chaco (dry forests and wet savannas), annual rainfall 450-1,200 mm (increasing from west to east), winter-summer temperatures 20-23°c; espinal (xerophitic forests), annual rainfall 400-1,000 mm (increasing from south to north), winter-summer temperatures 15-20°c; and monte (dry shrub-scrub steppe), annual rainfall 80-200 mm, winter-summer temperatures 13-17°c (bagno et al. 2004) . the vegetation within the range of l. braccatus is generally characterized by a mix of open grasslands to dense woodlands. seasonal precipitation, soil fertility, drainage, fire regime, and climatic fluctuations influence development of the different vegetative stages within the range of l. braccatus (bagno et al. 2004; de oliveira-filho and ratter 2002; trolle 2003) . along the transitional zone from grassland to woodland, various vegetative stages have been described. the stages of transition are campo limpo (clean field), a grassland with no shrubs or trees; campo sujo (dirty field), a grassland with a scattering of small trees and shrubs; campo cerrado (closed field), with tree cover of 30-900/0; and cerradao (dense woodland), the last stage almost completely covered with large trees and sparse ground-cover layer. leopardus braccatus gets its common name, pantanal cat, from the pantanal wetland complex, a 140,000-km 2 floodplain of the parana-paraguay watersheds. the pantanal is typified by a mosaic of the major biomes of central brazil, paraguayan chaco, and amazonian forest; a matrix of open fields interspersed with isolated patches of secondary forests and gallery forests border intermittent and permanent rivers (cavalcanti and gese 2009 ). the pantanal is almost totally inundated during the rainy season in october-march, with mean monthly precipitation of 145 mm; during the dry season in april-september, its mean monthly precipitation is only 48 mm. climate is seasonal, with warm, wet summers and cold, dry winters; wintersummer temperatures are 18-42°c (cavalcanti and gese 2009; trolle 2003) . when the pantanal is not seasonally flooded, many small water depressions are dispersed throughout its grasslands or forests. l. braccatus can be found among clumps of tall pampas grass in uruguay and in low-lying swampy areas (nowel and jackson 1996; silveira 1995; ximenez 1961) . l. braccatus has recently been found much farther north than previously recorded (de oliveira 2005 (de oliveira , 2006 , and rates of land conversion and fragmentation of available habitat in the pantanal are increasing (cavalcanti and gese 2009) , perhaps putting pressure on l. braccatus to seek out alternative habitats. diet.-leopardus braccatus appears to feed on ground birds, small mammals, and guinea pigs (cavia apereanowell and jackson 1996; silveira 1995) . stomach contents of 4 recent road-killed individuals contained small lizards and a colubrid snake (colubridae)-the 1st record of reptiles in the diet of l. braccatus. plant material, some beetles, and a small diurnal--erepuscular rodent also were found in the stomachs, suggesting nocturnal and diurnal activity of l. braccatus (bagno et al. 2004) . diseases and parasites.-no specific diseases have been reported for leopardus braccatus, but toxop/asma gondii, a parasitic protozoan responsible for toxoplasmosis in humans, was reported in a captive oncifelis (= leopardus) cotoco in brazil. little is known about what role wild felids have in the natural epidemiology of t. gondii, or as a cause of felid mortality or morbidity (silva et al. 2001) . two captive oncifelis (= leopardus) cotoco in north american zoos had active feline leukemia virus, and other captive brazilian pampas cats tested positive for the virus (filoni et al. 2003) . feline immunodeficiency virus and antibodies to feline coronavirus were reported in captive brazilian felids including oncifelis (= leopardus) cotoco (filoni et al. 2006) . antibodies of bartonella hense/ae (a proteobacterium) were found at very high prevalence in free-ranging brazilian felids, implying the cats act as a reservoir. b. hense/ae causes cat scratch disease in humans; fleas and ticks in the genus ixodes may serve as potential vectors for its transmission (filoni et al. 2006) . ticks (acari: ixodida) that occur primarily on horses and cattle also occur on carnivores in areas where the original vegetation has been replaced with cultivated pastures and are affected by other anthropogenic disturbances and fragmentation (labruna et al. 2005) . fungal dermatophytes that can lead to parasitic skin. infections and cause superficial mycoses in animals and humans have been found in asymptomatic healthy wild felids in captivity at fundacao par que zoologico de sao paulo, brazil. samples were taken from 130 adult animals of both sexes, including large, medium, and small cats; specifically, 8 oncifelis (= leopardusicoloco were confirmed as asymptomatic carriers and sources of potential infection for other animals and humans (bentubo et al. 2006) . many captive small felid species show some degree of skin disorders, traumatic lesions, enteritis, and dental disorders (filoni et al. 2003) . interspecific interactions.-leopardus braccatus is sympatric with other small felids such as l. tigrinus (oncilla or little tiger cat) and l. geoffroyi (geoffroy's catbagno et al. 2004; hemmer 1978; silveira 2005) . l. braccatus hybridized with l. tigrinus in areas of range overlap (cossios et al. 2009; . jaguars (panthera onca) are known to inhabit areas of the pantanal in argentina (soisalo and cavalcanti 2006) , and landscapelevel surveys in eastern paraguay revealed that small spotted cats such as l. braccatus avoid areas where jaguars occur (zuercher et al. 2001 ). the genus leopardus has a reduced number of diploid chromosomes (2n = 36), unlike other cat genera that have 38 chromosome pairs (collier and o'brien 1985; hemmer 1978; mattern and mclennan 2000; wayne et al. 1989 ). the unique metacentric chromosome, c3, in leopardus results from the fusion of 2 acrocentric f-group chromosomes. over the last decade, o'brien and colleagues performed genetic analyses on various aspects of the "pampas cat" genome (including but not limited to leopardus braeeatus), such as phylogenetic reconstruction, gene sequencing of both nuclear and mitochondrial dna, and protein electrophoresis (cossios et al. 2009; eizirik et al. 1998; johnson and o'brien 1997; masuda et al. 1996; mattern and mclennan 2000; napolitano et al. 2008; o'brien and yuhki 1999; pecon-slattery et al. 1994 pecon-slattery and o'brien 1998) . contrary to wozencraft (2005) and the suggestions of sunquist and sunquist (2009) , those molecular studies suggested that all species split by garcia-perea (1994) should be subspecies under l. eoloeolo. although o'brien and colleagues maintained confidence in the origins and blood lines of the samples collected and subsequently used in most genetic studies of l. eoloeolo (s. j. o'brien, pers. comm., 2010) , many of these samples were not collected from wild-caught individuals, but rather most samples were collected from individuals in various zoos; some with unknown histories or origins. this introduces some degree of uncertainty in taxonomic conclusions to date. genetic studies by identified hybrids in the general area of home-range overlap between a male l. braceatus and a female l. tigrinus; the hybrids displayed the tigrina pelage. trigo et al. (2008) performed further genetic investigations with an expanded data set and found more of the same hybridizations. one animal tested by trigo et al. (2008) was believed to be a hybrid in the opposite direction (mitochondrial dna from l. tigrinus introgressed into a l. eolocolo) documenting additional crossbreeding within the group; however, the origin and "race" of that animal was unknown. naturally occurring hybrids may come from areas of distributional overlap, and such individuals may exhibit morphological problems such as unusual penile structure and lack of spermatozoa in ejaculate, as was found in 1 adult male hybrid ). in brazil and argentina, leopardus braeeatus is considered "vulnerable." the international union for conservation of nature and natural resources lists the pampas cat group (= l. eoloeolo) as "near threatened" (pereira et al. 2008 ) because future population declines are likely to result from land conversion of native habitat to agricultural crops, land degradation from cattle grazing, fragmentation, hunting by local farmers in retaliation for depredation of their chickens, and decline of prey populations (bagno et al. 2004; cossios et al. 2009; soisalo and cavalcanti 2006; trolle 2003) . grazing in the pantanal has been shown to have adverse impacts on the environment; more specifically,forests in the pantanal are now dominated by invasive acuri palms (attalea phalerata) with little undergrowth and relatively little woody plant species (trolle 2003) . for conservation of l. braeeatus to be effective, morespecific information is needed about its distribution, population status, ecological requirements, and genetic diversity (lucherini et al. 2004 ). methods to monitor important habitats of l. braeeatus will continue to include camera-trapping (trolle 2003) , because the species is recognizable from its coat pattern (lucherini et al. 2004) . studies have shown genetic differences in alleles of l. braccatus and other closely related leopardus species trigo et al. 2008 ), but more basic research is needed on the systematics of south american small cats in general due to conflicting results from molecular and morphological studies (sunquist and sunquist 2009) . during the miocene, the climate of earth changed, resulting in pronounced ecological shifts in habitat characteristics and availability. as parts of south america became more arid and seasonal, the shrub-grassland steppe initially appeared as a continuum of habitats that changed from dense forests to open expanses. species no doubt adapted to these changes, but populations likely became isolated as preferred habitats became more disjunct. some species, such as l. braeeatus, probably started to exploit newly developing shrublands and grasslands, which provided novel prey (canepuccia et al. 2008; hemmer 1979) . amid current changes in global climate, precipitation regimes will become altered, and effects of habitat change on species abundance and biodiversity will be amplified, likely increasing emigration and adversely impacting survival . rates at the population level (canepuccia et al. 2008; hemmer 1979) . areas in argentina within the current range of l. braceatus have experienced an increase in annual precipitation of 10-300/0 over the last 50 years (canepuccia et al. 2008 ). l. braeeatus may face greater threats in lowlying areas with increased precipitation, given that most native uplands have been converted to agriculture (as much as 800/0 of the cerradobagno et al. 2004 ) and are used for grazing. these effects can adversely impact populations, both directly and indirectly, by altering fitness and modifying availability of resources. prey abundance may be reduced, and den sites may be lost to flooding. these interactions suggest that global climatic patterns could have significant negative impacts at regional and local population scales (canepuccia et al. 2008) . to foster the conservation of l. braceatus, the following actions might be beneficial: reduce loss of native habitat to agriculture; identify populations and metapopulations of l. braccatus across its entire range; create conservation areas to minimize further habitat loss and public outreach programs to educate people about the species and its needs; and generally increase awareness of the vulnerability of all speciesin this part of south america. furthermore, additional genetic research on wild-caught individuals could help validate or refute earlier genetic research performed on largely captive animals. reports of the princeton university expeditions to patagonia severtzow's classification of the felidee notes on the synonymy and nomenclature of the smaller spotted cats of tropical america uber felis braccata cope und andere schonbrunner kleinkatzen notes on the natural history and conservation status of pampas cat, oncifelis colocolo, in the brazilian cerrado isolation of microsporum gypseum from the haircoat of healthy wild felids kept in captivity in brazil a new species of small cat (felidae) from the late pliocene-early pleistocene (uquian) of argentina gradual miocene to pleistocene uplift of the central american isthmus: evidence from tropical american tonnoidean gastropods notas sobre carnivoros sudamericanos mamiferos sud-americanos, vida, costumbres y descripcion mammals. from mato grosso do sui, brazil; lists of species differential response of marsh predators to rainfall-induced habitat loss and subsequent variations in prey availability spatial ecology and social interactions of jaguars (panthera onca) in the southern pantanal confirmacion de la presencia del gato del pantanal lynchailurus braccatus (cope, 1889) en la argentina the geologic evidence of the central american isthmus. pp. 21-56 in evolution and environment in tropical a molecular phylogeny of the felidae: immunological distance on the mammalia obtained by the naturalist exploring expedition to southern brazil descrizione di una nuova specie del genere: felis. felis jacob ita (com.). memorie della influence of ancient glacial periods on the andean fauna: the case of the pampas cat (leopardus colocolo) update on the distribution of the andean cat oreailurus jacob ita and the pampas cat lynchailurus colocolo in peru a new record of pampas cat, lynchailurus braccatus, in brazil wild cats of brazil projectlprojeto gatos do mato-brasil. cat project of the month-july. international union for conservation of nature and natural resources/species survival commission cat specialist group feature project of the month project wild cats of brazil vegetation physiognomies and woody flora of the cerrado biome in the cerrados of brazil: ecology and natural history of a neotropical savanna cuv. pp. 73-123 in nouveau dictionnaire d'historie naturelle, applique aux arts, a l'agriculture, a l'economie rurale et domestique, a la medicine, etc. par une societe de naturalists et d'agriculteurs, nouv mammalogie: nouvelle espece de felis phylogeographic patterns and evolution of the mitochondrial dna control region in two neotropical cats (mammalia, felidae) serosurvey for feline leukemia virus and lentiviruses in captive small neotropic felids in sao paulo state, brazil first evidence of feline herpesvirus, calicivirus, parvovirus, and ehrlichia exposure in brazilian free-ranging felids revision der zur natiirlichen familie der katzen (feles) gehorigen formen phylogeny of the carnivora descriptiones animalium: avium, amphibiorum, piscium, insectorum, vermium; que in itinere orientali (post mortem auctoris carsten niebuhr) the pampas cat group (genus lynchailurus severtzov, 1858) (carnivora: felidae), a systematic and biogeographic review leopardus braccatus geoffroy saint-hilaire, i. 1844. voyages dans l'inde par v. jacquemont, pendant les annees 1828 it 1832. tome vi. part 2. didot freres a new genus of eulophidae from the united states leopardus cotoco (on-line) descriptions of some new genera and fifty unrecorded species of mammalia notes on the skulls of the cats (felidae) the evolutionary systematics of living felidae: present status and current problems fossil history of the living felidae the naturalist's library resolution of recent radiations within three evolutionary lineages of felidae using mitochondrial restriction fragment length polymorphism variation phylogenetic reconstruction of the felidae using 16s rrna and nadh-5 mitochondrial genes disparate phylogeographic patterns of molecular genetic variation in four closely related south american small cat species the late miocene radiation of modem felidae: a genetic assessment disparate phylogeographic patterns of molecular genetic variation in four closely related south american small cat species fossilium catalogus animalia. index generum et subgenerum mammalium ticks (acari: ixodida) on wild carnivores in brazil systema naturae per regna tria nature, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. tomus i. editio decima, reformata. impensis direct laurentii salvii mantissa plantarum altera generum editionis vi et specierum ii a preliminary revision of knowledge status of felids in argentina molecular phylogeny of mitochondrial cytochrome band 12s rrna sequences in the felidae: ocelot and domestic cat lineages phylogeny and speciation of felids notes on some mammals of southern matto grosso saggio sulla storia naturale de chili ecological and biogeographical inferences of two sympatric and enigmatic andean cat species using genetic identification of faecal samples revisao taxonomica do genero leopardus gray, 1842 (carnivora, felidae) wild cats: status survey and conservation action plan. international union for conservation of nature and natural resources the evolution of cats comparative genome organization of the major histocompatibility complex: lessons from the felidae phylogenetic reconstruction of south american felids defined by protein electrophoresis patterns of y and x chromosomes dna sequences divergence during the felidae radiation phyolgenetic assessment of introns and sines within the y chromosome using the cat family felidae as a species tree novel gene conversion between x-y homologues located in the nonrecombining region of the y chromosome in felidae (mammalia) leopardus cotocoto, international union for the conservation of nature and natural resources red list of threatened species. international union for the conservation of nature and natural resources carnivores (mammalia, carnivora) from the quaternary of serra da bodoquena, mato grosso do sui, brazil. arquivos do museu nacional the classification of existing felidae the examples of the coloco and of the pampas cat in the british museum new material of pleistocene cats (carnivora, felidae) from southern south america with comments on biogeography and the fossil record felid phylogenetics: extant taxa and skull morphology (felidae, aeluroidea) nuevo registro de oncife/is cotoco (felidae) para el pantanal de brasil das thierreich eingetheilt nach dem bau der thiere als grundlage ihrer naturgeschichte und der vergleichenden anatomie von dem herm ritter von cuvier die saugethiere in abbildungen nach der natur, mit beschreibungen siidamerikanische busch-, berg-und steppenkatzen cats: the smithsonian answer book notice sur la classification multieriale des carnivores, specialement des felidedes, et les etudes de zoologie generale qui s'y rattachent seroprevalence of toxop/asma gondii in captive neotropical felids from brazil notes on the distribution and natural history of the pampas cat, felis cotocoto, in brazil carnivore population ecology in cerrado environment. jaguar conservation fund estimating the density of a jaguar population in the brazilian pantanal using cameratraps and capture-recapture sampling in combination with gps radio-telemetry wild cats of the world family felidae (cats). pp. 54-169 in handbook of the mammals of the world lynx edicions notes on the neotropical mammals of the genera felis, hapale, oryzomys, akodon, and ctenomys, with descriptions of new species inter-species hybridization among neotropical cats of the genus leopardus, and evidence for an introgressive hybrid zone between l. geoffroyi and l. tigrinus in southern brazil mammal survey in the southeastern pantanal die saugethiere in abbildungen nach der nature mit beschreigungen. supplementband 2. bob'schen molecular and biochemical evolution of the carnivora abbildungen zur naturgeschichte von brasilien order carnivora. pp. 532-628 in mammal species of the world: a taxonomic and geographic reference new subspecies of pampas cat from uruguay, felis colocolo muiioai. communicaciones zoologicas del museo de a predator-habitat assessment for felids in the inland atlantic forest of eastern paraguay: a preliminary analysis pamela owen reviewed the fossil account and sergio solari and alfred gardner reviewed the synonymies. associate editor and editor of this account was key: cord-312267-0tb08b0z authors: freitas, a. s.; silva, l. s.; sandes, s. s. l. title: new s.i.r. model used in the projection of covid 19 cases in brazil date: 2020-05-01 journal: nan doi: 10.1101/2020.04.26.20080218 sha: doc_id: 312267 cord_uid: 0tb08b0z in this work, we proposed a variant of the sir model, taking as based on models used to describe the epidemic outbreak in south korea and portugal, to study the sars-cov-2 epidemic curve in brazil. the model presented here describes with reasonable agreement the number of covid-19 cases registered in brazil between february 26 and april 25, 2020 based on the hypothesis that there a large number no notified cases (11 to 1) and variation in contagion rate according to social isolation measures and greater or lesser exposure to the virus (highest rate in beginning from epidemic). to this end, we introduced an exposure factor, called {beta}1/{beta}2, which allows us to describe the influence of factors such as social isolation on dispersal from disease. the results also corroborate a phenomenon observed in countries that registered a high growth in cases in short period of time, to example of italy, spain and usa: if isolation measures are imposed late, the total number of cases explodes when the epidemic is approaching from peak, which implies a higher exposure rate in the first days of case registration. the model also predicts that the peak epidemic outbreak in brazil, based on the number of cases, will occur around may 20, 2020. since the outbreak of the disease covid-19 in the city of wu han, china, in just over two months the epidemic spread rapidly around the world, until that on march 11, 2020, the world health organization (who) declared the covid-19 pandemic (zhang et al., 2020) . until april 25, 2020 the number of cases in the world had already exceeded 3 million, with approximately 200.000 confirmed confirmed deaths. with the explosion in number of cases from covid-19 in brazil and worldwide, to understand how it happens the evolution of the number of cases is important to evaluate the measures taken until the moment were effective, as well to determine the next actions to be executed in order to prevent the collapse of the country's health system. in 1927, w. o. kermack and a. g. mckendrick (1927) created a model that considers a fixed population with only three compartments: sensitive, s (t); infected, i (t), and removed, r (t) -sir (susceptible-infected-recovered) -for the first time, in order to study the evolution of epidemic processes and how the spread of infectious diseases over time . other models were created along the history, for example one developed by daniel bernoulli in 1790 to study the variola epidemic (herben, 2000) . the s.i.r model allows to project the evolution of an infectious disease in a population in agreement with their state transition rates and their initial conditions s(0), i(0) and r(0) and it gets, with reasonable precision, to describe quantitatively, for instance, the time interval from the first contagion until the number of infected people reaches the epidemic peak, important information that allows governments to develop actions to reduce the number of having infected or, at least, extend the time in that peak of infections will be reached (schimit, 2010; jo, 2020) . however, there are variants of the sir model that can be applied in situations in which another variables are important for description how the infection spreads in a population of s susceptible individuals, to example as was done in teles' work (2020) adapting the sir model to describe the behavior of the coronavirus infected curve in portugal. in this work, we propose a variation of the sir model, taking initially described by jo et al. work (2020) , to describe the projection of cases of covid-19 in a qualitative and quantitative way in brazil since the first day in wich cases were confirmed, february 26, 2020, until april 25, 2020. for this, we will use what here we will call sier model, susceptible-infect-exposed-recovered, that is, a model that also considers that there exposed individuals, represented by the e(t) function, which have a higher probability of infection than average populational. in the following sections, we will present the model and the method used to solve the differential equations originating from it; then we will present the results obtained, following by the final considerations. in this work a variant of the s. i. r. model -susceptible, infected and removed (recovered and/or died), with fixed number for the population (normalized, n=1), without taking into account the amount of births/deaths, but taken into account that, in the universe from susceptible individuals, s(t), there is a smaller number of individuals e(t), that are those susceptible, however more exposed to infection, to example of people that be not able to adhere the complete social isolation or professionals of health, that are in frontline from caring of those infected. the model takes into account that a s(t) -e(t) number of individuals can be infected at rate β 1 and a e(t) number of individual can be infected a rate β 2 >β 1 , once the exposed individuals have larger probability to contract the virus and infect other individuals. the functions that represent the susceptible individuals, s(t), infected, i(t), exposed, e(t), and removed/recovered, r(t), are link with their respective rates of temporal variation from the system of differential equations (to a time t > 0): . 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 certified by peer review) the copyright holder for this preprint this version posted may 1, 2020. . where γ is the average recovery rate (1/γ is the period during which the infection continues), and the functions s(t), i(t), e(t) and r(t) obeying the following conditions: is the effective contagion rate (with n = 1). this model is appropriate for diseases that spread quickly and give immunity to survivors, to example as the flu (schimit, 2010), but can, without loss of generality, be used to describe the installation of agricultural pests or spread of computer virus. in most varied lattices topologies, for instance, since the propagation processes, of the disease or information, are very similar (hastings, 2003; pachi, 2006) . there are other models that take into account differences between the propagation mechanisms or even larger complexity in the individuals interaction, but they will not be treated in this work. the eqs. (1) are of difficult analytical resolution, what takes to approaches or it looks for numeric treatment to arrive to the curves that represent s(t), i(t), e(t) and r(t). to this, a computational routine was developed for language octave with the intention of obtain the numeric solutions for that model and to apply it to study spread of covid-19 in brazil, without considering the differences of each place. octave is a software of free distribution, following the patterns of distribution of the general public license (gnu), with several functions for resolution systems of differential equations for instance (scherer, 2005) . here, we suppose that all individuals belonging to population have equal contracting / transmitting probability the disease in certain time interval (keeling, rohani, 2008; newmann, 2002) . the presented results will be analyzed according with the following premises: i) the number of cases is, at least, eleven times greater than that officially registered (walker et al., 2020) ; ii) the rate of contagion doesn't vary with time and is the same for all individuals; iii) the relationship among β 1 and β 2 parameters, specifically the ratio β 1 / β 2 , is the important coefficient for analysis from impacts of high exposure to virus and its consequences in which concerns the spread of infection by population; iv) the absence of politics of social isolation (high exposure from relatively large portion of population) implies more, in our analysis, a greater number of cases than a significant change at time when the epidemic curve reaches the peak maximum. . 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 this version posted may 1, 2020. . fig. 1 shows the behavior of the curves of infected and exposed individuals (that still didn't contract the disease) in function time, in agreement with the model proposed in this wo qualitative way, however there is slight dependence between the date which the peak of infection occurs and total percentage of infected (number of accumulated cases) at the peak of infection: the larger infected and if the total number of infected is greater (especially in the epidemic peak), the impact on health system is considerably greater (taking into account the same rate of contagion in two cases) . it`s observed that there is no significant difference in the number of cases at beginning from epidemic, independent of greater number or not from highly exposed susceptible individuals. this characteristic has been observed in several countries, especially in those where politics of social isolation were not initially imposed. in the beginning of the outbreak, governments that did not adopt isolation politics because, apparently, the epidemic outbreak had lost force, were eventually forced to adop once the cases number exploded after a short period of time, and this is exactly the behavior visualized in the epidemic curves shown in fig. 1 . the graphs from figures 2 and 3 shows the epidemic curve for different scenarios, with slightly different β we have the variation in number of infected individuals (percentage of infected in the graph in fig. 1 shows the behavior of the curves of infected and exposed individuals (that still didn't contract the disease) in function time, in agreement with the model proposed in this work. the curves show a typical epidemic pattern, in a qualitative way, however there is slight dependence between the date which the peak of infection occurs and total percentage of infected (number of accumulated cases) at the peak of infection: the larger contagion factor β 1 /β 2 , the larger the total number from infected and if the total number of infected is greater (especially in the epidemic peak), the impact on health system is considerably greater (taking into account the same rate of it`s observed that there is no significant difference in the number of cases at beginning from epidemic, independent of greater number or not from highly exposed susceptible individuals. this characteristic has been observed in several countries, especially in those where politics of social isolation were not initially imposed. in the beginning of the outbreak, governments that did not adopt isolation politics because, apparently, the epidemic outbreak had lost force, were eventually forced to adop once the cases number exploded after a short period of time, and this is exactly the behavior visualized in the epidemic curves shown in fig. 1. . curve showing the number (percentage) of infected and exposed individuals in time function to different values from exposure factor, β 1 /β 2 . the graphs from figures 2 and 3 shows the epidemic curve for different scenarios, with slightly different β 1 /β 2 ratios, as well as different contagions. in figure 1 we have the variation in number of infected individuals (percentage of infected in the graph in fig. 1 shows the behavior of the curves of infected and exposed individuals (that still didn't contract the disease) in function time, in agreement with the rk. the curves show a typical epidemic pattern, in a qualitative way, however there is slight dependence between the date which the peak of infection occurs and total percentage of infected (number of accumulated cases) at the , the larger the total number from infected and if the total number of infected is greater (especially in the epidemic peak), the impact on health system is considerably greater (taking into account the same rate of it`s observed that there is no significant difference in the number of cases at beginning from epidemic, independent of greater number or not from highly exposed susceptible individuals. this characteristic has been observed in several countries, especially in those where politics of social isolation were not initially imposed. in the beginning of the outbreak, governments that did not adopt isolation politics because, apparently, the epidemic outbreak had lost force, were eventually forced to adopt them, once the cases number exploded after a short period of time, and this is exactly the . curve showing the number (percentage) of infected and exposed individuals in time the graphs from figures 2 and 3 shows the epidemic curve for different ratios, as well as different contagions. in figure 1 we have the variation in number of infected individuals (percentage of infected in . 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 this version posted may 1, 2020. . https://doi.org/10. 1101 relation to the whole brazil population (210.147.125 people more than sixty days as time fun figure 2 . epidemic curves for several scenarios, with different contagion rates and exposure factors. using the hypothesis that there are eleven cases for each case officially notified in brazil (walker et al., 2020) . the curve that best fits the case number registered in the country between february 26 and april 25, 2020 is to contagion factor equal to 2.0. the graph shows, taking into account the contagion rate curve 2.0, that the epidemic peak will be reached around may 20, 2020. data available at: coronavírus brasil, https://covid.saude.gov.br/ the epidemic curve in fig. 2 present a compatible pattern with infection models with exponential growth during the initial period, change in the concavity of curve that describes the number of infected, i(t), until reaching the peak, for a given percentage cases, and the decrease from accumulated amount from registered cases. interesting to observe that, using the hypothesis that there are eleven cases for each officially notified case in brazil (walker registered in the country between february 26 and april 25, 2020 is that to contagion factor is equal to 2.0. it`s also observed that one that more influences in the fast initial virus spread is the contagion rate, serving the exposure factor β differentiate the speed with which the epidemic will spread taking into account a same contagion rate. for instance, if the contagion rate is high, even with a low β exposure factor, the epidemic spreads quickly. the graph in fig. 2 displ account the contagion rate curve 2.0, that the epidemic peak will be reached around may 20, 2020, but is important have caution about this data, once brazil is a country relation to the whole brazil population (210.147.125 people -ibge, 2019) along little more than sixty days as time function. epidemic curves for several scenarios, with different contagion rates and exposure factors. using the hypothesis that there are eleven cases for each case officially notified in brazil (walker et al., 2020) . the curve that best fits the case ered in the country between february 26 and april 25, 2020 is to contagion factor equal to 2.0. the graph shows, taking into account the contagion rate curve 2.0, that the epidemic peak will be reached around may 20, 2020. data available https://covid.saude.gov.br/. the epidemic curve in fig. 2 present a compatible pattern with infection models with exponential growth during the initial period, change in the concavity of curve that describes the number of infected, i(t), until reaching the peak, for a given percentage cases, and the decrease from accumulated amount from registered cases. interesting to observe that, using the hypothesis that there are eleven cases for each officially notified case in brazil (walker et al., 2020) , the curve that best fits the number registered in the country between february 26 and april 25, 2020 is that to contagion factor is equal to 2.0. it`s also observed that one that more influences in the fast initial virus spread is the contagion rate, serving the exposure factor β 1 /β differentiate the speed with which the epidemic will spread taking into account a same contagion rate. for instance, if the contagion rate is high, even with a low β exposure factor, the epidemic spreads quickly. the graph in fig. 2 displ account the contagion rate curve 2.0, that the epidemic peak will be reached around may 20, 2020, but is important have caution about this data, once brazil is a country ibge, 2019) along little epidemic curves for several scenarios, with different contagion rates and exposure factors. using the hypothesis that there are eleven cases for each case officially notified in brazil (walker et al., 2020) . the curve that best fits the case ered in the country between february 26 and april 25, 2020 is to contagion factor equal to 2.0. the graph shows, taking into account the contagion rate curve 2.0, that the epidemic peak will be reached around may 20, 2020. data available the epidemic curve in fig. 2 present a compatible pattern with infection models with exponential growth during the initial period, change in the concavity of curve that describes the number of infected, i(t), until reaching the peak, for a given percentage of cases, and the decrease from accumulated amount from registered cases. interesting to observe that, using the hypothesis that there are eleven cases for each officially notified , 2020), the curve that best fits the number of cases registered in the country between february 26 and april 25, 2020 is that to contagion factor is equal to 2.0. it`s also observed that one that more influences in the fast initial /β 2 as a way to differentiate the speed with which the epidemic will spread taking into account a same contagion rate. for instance, if the contagion rate is high, even with a low β 1 /β 2 exposure factor, the epidemic spreads quickly. the graph in fig. 2 display, taking into account the contagion rate curve 2.0, that the epidemic peak will be reached around may 20, 2020, but is important have caution about this data, once brazil is a country . 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 this version posted may 1, 2020. . from continental dimensions, with important regional differences that each state will reach the peak in different dates. in fig. 3 have the percentage data of infected people over thirty days, considering the first thirty days starting from the first case registered in brazil (february 26, 2020, day 1) until april 25, 2020. can be observed in this graph that the number of cases (hypothesis of eleven for each registered case) in brazil increase with a contagion rate close in 2.0 in the first thirty days from epidemic outbreak, dropping to 2.0 after thirty days, indicating that measures of social isolation adopted in the country, even if partially, served to reduce the speed of spread from virus, even with different rates of beta exposure, which indicates that the ideal is to combine the rates of contagion and exposure this way we have a real picture how the epidemic is spreading. it`s evident that contagion isn`t fixed in time and depends strongly on isolation measures: in the beginning from pandemic, with many exposed individuals, the contagion is high and can remain so (or even increase) if no measure of social isolation is adopted , falling continuously with time, because a combination of isolation measures with factors such as climate and seasonal diseases. for instance, in winter, flu syndromes are more common, which ends up taking more people to hospitals (increased exposure rate). going to hospitals, these people are subject to contact with other individuals infected by coronavirus, fact that increases the contagion chance both for those have another type of comorbidity and for their companions from continental dimensions, with important regional differences that may indicate that each state will reach the peak in different dates. in fig. 3 have the percentage data of infected people over thirty days, considering the first thirty days starting from the first case registered in brazil (february l april 25, 2020. can be observed in this graph that the number of cases (hypothesis of eleven for each registered case) in brazil increase with a contagion rate close in 2.0 in the first thirty days from epidemic outbreak, dropping to 2.0 after s, indicating that measures of social isolation adopted in the country, even if partially, served to reduce the speed of spread from virus, even with different rates of beta exposure, which indicates that the ideal is to combine the rates of contagion and exposure this way we have a real picture how the epidemic is spreading. it`s evident that contagion isn`t fixed in time and depends strongly on isolation measures: in the beginning from pandemic, with many exposed individuals, the remain so (or even increase) if no measure of social isolation is adopted , falling continuously with time, because a combination of isolation measures with factors such as climate and seasonal diseases. for instance, in winter, flu e common, which ends up taking more people to hospitals (increased exposure rate). going to hospitals, these people are subject to contact with other individuals infected by coronavirus, fact that increases the contagion chance both for type of comorbidity and for their companions . curves with the percentage of infected (in relation to the total brazilian population) in an interval of 55 days. may indicate that in fig. 3 have the percentage data of infected people over thirty days, considering the first thirty days starting from the first case registered in brazil (february l april 25, 2020. can be observed in this graph that the number of cases (hypothesis of eleven for each registered case) in brazil increase with a contagion rate close in 2.0 in the first thirty days from epidemic outbreak, dropping to 2.0 after s, indicating that measures of social isolation adopted in the country, even if partially, served to reduce the speed of spread from virus, even with different rates of beta exposure, which indicates that the ideal is to combine the rates of contagion and exposure this way we have a real picture how the epidemic is spreading. it`s evident that contagion isn`t fixed in time and depends strongly on isolation measures: in the beginning from pandemic, with many exposed individuals, the remain so (or even increase) if no measure of social isolation is adopted , falling continuously with time, because a combination of isolation measures with factors such as climate and seasonal diseases. for instance, in winter, flu-like e common, which ends up taking more people to hospitals (increased exposure rate). going to hospitals, these people are subject to contact with other individuals infected by coronavirus, fact that increases the contagion chance both for . curves with the percentage of infected (in relation to the total brazilian the real data from pandemic is very underreported, a rising carried out by open knowledge brasil (2020) , organization that act in the area of transparency and openness from public data, in evaluation that considered the content, format and level of detail from information published on the portals from state governments and federal government; 11 brazilian states do not publish minimum data, in which 90% of the evaluated states, until april 3, 2020, still did not publish enough data to accompany the spread from covid-19 pandemic across country, including the federal government. like this, any scenario drawn by mathematical systems based on government data can`t represent the real situation of the pandemic in brazil. in addition, until april 2, 2020, more than 25 thousand tests for covid-19 were still waiting for results, a number three times higher than the number of confirmed cases until that date. considering that the ministry of health from brazil recommends testing only severe cases, considering that tests are still lacking even for severe cases, added to fact that large part from population is asymptomatic for covid-19, we noticed that the number of underreported cases in brazil it is extremely underestimated, which reinforces the hypothesis adopted here, based on the study by walker et al. (2020) eleven cases for each made registration. the analysis of the behavior from epidemic curves shown in the graph in fig. 3 ensures the validity of one of our hypotheses, that the contagion rate in brazil is between 2.0 and 3.0. if no measure of social distancing or decrease in exposure the contaminated was adopted, the contagion rate could be higher than 3.0. is important to express that the curves modeled by the s.i.r. model not consider crucial factors that can lead to even worse panoramas, such as, for instance, the virus is already present in slums in brazil, where more than 13 million people live, according to the locomotiva institute (2020). in these places, families live in just one room, being impossible to separate risk groups, such as senior, from people who need to go out to work and return home, increasing the risk of contamination. in many of these communities, there no are basic sanitation conditions are, impending simple processes such as hand hygiene frequently, as recommended by authorities. in summary, the model presented here describes with reasonable agreement the number of cases from covid-19 registered in brazil between february 26 and april 25, 2020 with based on hypothesis that there a large number of underreported cases (11 to 1) and variation in the contagion rate of according to measures of social isolation and greater or lesser exposure to the virus (higher rate at the beginning of the epidemic). the results also corroborate with a phenomenon observed in countries that registered a high growth in cases in a short period of time, such as italy, spain and the usa: if isolation measures are imposed late, the total number of cases explodes in way epidemic is approaching from maximum peak, which implies a higher exposure rate in the first days of case registration. the model also predicts that the peak epidemic outbreak in brazil, based on the number of cases, will occur around may 20, 2020. science . v 299. p. 2003-2004. 2003 . . 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 certified by peer review) the copyright holder for this preprint this version posted may 1, 2020. . https://doi.org/10. 1101 the mathematics of infectious diseases analysis of covid-19 spread in south korea using the sir model with time-dependent parameters and deep learning contributionstothemathematicaltheoryof epidemics spread of epidemic disease on networks modelo matemático para o estudo da propagação de informações por campanhas educativas e rumores modelagem e controle de propagação de epidemias usando autômatos celulares e teoria dos jogos métodos computacionais da física. 1ª ed. editora livraria da física predicting the evolution of sars-covid-2 in portugal using an adapted sir model previously used in south korea for the mers outbreak the global impact of covid-19 and strategies for mitigation and suppression the use ofanti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (covid-19): the experience of clinical immunologists from china key: cord-283291-lj3k53px authors: brugnago, eduardo l.; silva, rafael m. da; manchein, cesar; beims, marcus w. title: how relevant is the decision of containment measures against covid-19 applied ahead of time? date: 2020-08-12 journal: chaos solitons fractals doi: 10.1016/j.chaos.2020.110164 sha: doc_id: 283291 cord_uid: lj3k53px the cumulative number of confirmed infected individuals by the new coronavirus outbreak until april 30(th), 2020, is presented for the countries: belgium, brazil, united kingdom (uk), and the united states of america (usa). after an initial period with a low incidence of newly infected people, a power-law growth of the number of confirmed cases is observed. for each country, a distinct growth exponent is obtained. for belgium, uk, and usa, countries with a large number of infected people, after the power-law growth, a distinct behavior is obtained when approaching saturation. brazil is still in the power-law regime. such updates of the data and projections corroborate recent results regarding the power-law growth of the virus and their strong distance correlation between some countries around the world. furthermore, we show that act in time is one of the most relevant non-pharmacological weapons that the health organizations have in the battle against the covid-19, infectious disease caused by the most recently discovered coronavirus. we study how changing the social distance and the number of daily tests to identify infected asymptomatic individuals can interfere in the number of confirmed cases of covid-19 when applied in three distinct days, namely april 16(th) (early), april 30(th) (current), and may 14(th) (late). results show that containment actions are necessary to flatten the curves and should be applied as soon as possible. how relevant is the decision of containment measures against covid19 applied ahead of time? since the first infection of the coronavirus in december 2019, observed in wuhan (china), the virus has spread around the world very quickly and nowadays 215 countries, areas, or territories 1 report confirmed cases of the infection. innumerable scientists in distinct areas are using their knowledge in the battle against the still evolving covid-19 outbreak around the globe. the daily analysis of data about the spreading of the virus and possible interpretations that allow us to track and control the virus are of most relevance. it is a timely appeal to find explanations and models which may allow email addresses: elb@fisica.ufpr.br (eduardo l. brugnago 1 ), rmarques@fisica.ufpr.br (rafael m. da silva 1 ), cesar.manchein@udesc.br (cesar manchein 2 ), mbeims@fisica.ufpr.br (marcus w. beims 1 ) 1 "territories" include territories, areas, overseas dependencies and other jurisdictions of similar status [1]. us to understand the evolution of the viruses better, saving lives and avoiding economic and social catastrophes [2] . in the battle against the covid-19 spreading, some models focus on the geographical spread of the virus [3, 4] , while others remain restricted to a given area, or country, but analyze the local temporal development of the epidemic. in the context of diseases, in 1760, daniel bernoulli proposed a mathematical model of disease propagation and showed the efficiency of the preventive inoculation technique against smallpox [5] . this model included susceptible and immune individuals [6] . later on, kermack and mckendrick [7] came up with the susceptible-infected-recovered (sir) model. during the last years, other more sophisticated models have been proposed like the delayed sir epidemic model [8] , the susceptible-exposed-infected-recovered (seir) model [9, 10, 11] and its modified versions [12, 13, 14, 15, 16] . both approaches, brazil, (c) uk, and (d) usa, excluding days with less than 100 infected. the black-continuous curves represent the function ∝ t µ that fit the time-series, with exponent µ for each country. the insets display the same curves but in the log-log plot. the geographical spread, and the local temporal evolution, are of most relevance. more recently, the use of heterogeneous effects in the sir model [17] and the viral infections in the presence of latently infected cells [18] have been analyzed. while the present work focuses on non-pharmacological containment measures, in the battle against the covid-19, studies about the use of ivermectin are in progress [19] , a drug used in malaria spreading scenarios which allows the transition from the prevalence to the eradication of the disease [20] . it is well-known that the decisive quantity used to regulate the dynamical evolution of epidemics, in general, is the average reproductive number r 0 , which gives the number of secondarily infected individuals generated by a primary infected individual. while for values r 0 < 1 the number of newly infected individuals decreases exponentially, for 1 < r 0 < ∞ it increases exponentially [21, 22] . starting from the primordial exponential solution put up by verhulst in 1838, the well known logistic model for the law of population growth [23] , models were improved more and more in the last decades to better describe the nonlinear and complex comportments which occur in our environment. in fact, in many realistic systems, power-law functions are the law of growth (or decrease), as in the branch-ing processes with a diverging reproductive number [21] , in scale-free networks and small worlds [24] , and in foraging in biological systems [25] . indeed, recent investigations showed a power-law growth of the cumulative number of infected individuals by the new coronavirus [12, 13, 26, 27] , which might be typical of small world networks [28] and possibly related to fractal kinetics and graph theory [29] . recently, we have shown that power-law growth is observed in countries from four distinct continents [12] until march 27 th , 2020. the considered countries were: brazil, china, germany, italy, france, japan, spain, the republic of korea, and the united states of america (usa). one leading observation was that after an initial time with a low incidence of newly infected people, the growth of the cumulative number of confirmed cases for all studied countries followed a power-law. the distance correlation [30, 31, 32, 33] between these countries was found to be very strong and suggest a universal characteristic of the virus spreading. one of the goals of the present work is to update to april 30 th , 2020 the time-series analysis for the covid-19 growth for the countries brazil and usa. we included belgium and united kingdom (uk) on this list and leave out the other countries which are reaching the saturation regime. meaning initial condition n country population. depends on the country s individuals susceptible to infection. exposed individuals, latent cases. adjusted from data i s symptomatic infectious cases. i s (t 0 ) = c(t 0 ) i a asymptomatic and mild infectious cases. . we call to attention that the values in the vertical axis in fig. 1 change for different countries. initial data, regarding the days with less than 100 infected individuals, were discarded. the black-continuous curves represent the function ∝ t µ that fits the time series, and the exponent µ for each country is indicated in each panel. the insets display the same curves but in the log-log plot. straight lines in the log-log plot indicate power-law growth. the only country for which the power-law growth still takes place is brazil, as shown in fig. 1(b) . the reason is that it is still away from the saturation point. this is different for belgium, uk, and usa, as can be seen in figs. 1(a), 1(c), and 1(d), respectively. dashed-black lines in these three panels are projections in case the powerlaw would have guided the growth. besides the above updates, in this paper, we describe in detail the modified seir model which was used recently [12] to propose strategies to flatten the power-law curves. it is shown how to adjust the parameters of the model to real data. furthermore, using the same model we discuss what would be the effect of early, current, and late non-pharmacological actions to flatten the curves of the four countries shown in fig. 1 . this clearly shows that each day lost by delaying non-pharmacological actions can cost many lives. the paper is divided as follows. in sec. 2, we present in detail the model used in this work. section 3 discusses the effect of containment actions on the total number of confirmed infected cases applied in three distinct days and sec. 4 summarizes our results. in this section we describe in detail the model used to reproduce the realistic data of the who and to predict the effect of strategies used to flatten the power-law curves. the model that we used is the modified seir model described by the following six ordinary differential equations (odes) [12] in addition to these equations, we compute the cumulative number of confirmed cases c of covid-19 from the following ode: through this variable, the parameters (θ, κ s ) can be adjusted, as described later on. table 1 brings together all variables and parameters of the model and their meaning. in the case of the variables, the initial conditions are also presented and in the case of the parameters, the predefined values obtained from preceding studies are also listed. the highlight lines in table 1 call to attention to the variable c, which is the main quantity analyzed in this work, to the adjustable parameters θ and κ s , and to the strategic parameter κ a . after the adjustment, the parameters θ and κ a will be varied to give rise to specific strategies. worth to mention that θ = γr 0 , where r 0 is the basic reproductive number without social distance actions, and γ is the interaction factor between individuals. this factor comprises the parameters of isolation and social interaction. larger social distance implies smaller values of θ, which is equivalent to reduce r 0 . the distinction between θ and r 0 allows us to identify the direct effects of the actions in the battle against the pandemic. thus, the ideal situation would be to find θ < 1. condensing the explanation of the schema, starting from the left, susceptible individuals s develop into exposed individuals e by a rate θ(i s + αi a )/(n t inf ) which, after a latent time t lat , become symptomatic i s or asymptomatic i a with the rate (1 − β)/t lat and β/t lat , respectively. applying daily tests in a rate κ s (κ a ) to identify symptomatic (asymptomatic) infected individuals, they are immediately sent to quarantine q, staying there for a time t ser before recovering (r). on the other hand, infected individuals who have not been tested are sent to the class r after the infection time t inf . since no vaccine has been developed until today, the model does not contain an immunization term. no rigid quarantine is taken into account. furthermore, in eq. (5), the factor t ser dividing q represents a rate of exit from the quarantine (to the group r). from the dynamical point of view, the model is non-chaotic. this allows us to discuss the asymptotic behavior of the relevant quantities. in fact, multigroup epidemiological models of seir type have been shown, in general, to be asymptotically stable [35, 36] . the fixed point is found by assuming zero for all time derivatives of the variables in the epidemiological model, furnishing (s * , e * , i * s , i * a , q * , r * ) = (s * , 0, 0, 0, 0, n − s * ), as well as the total number of confirmed cases goes to c * , where the stars denote the fixed point and s * and c * depend on initial conditions and parameters. for s * = 0 we have r * = n and for s * = 0 we obtain r * = n −s * . since all variables and parameters from the model are positive, from eq. (1) we realize that s(t) always decreases and that asymptotically lim t→∞ s(t) = s * ≥ 0. furthermore, it is possible to rewrite eq. (2) as thus, for sufficently small values of ds/dt close to s * , e(t) decreases exponentially and lim t→∞ e(t) = e * = 0. with a similar analysis we conclude that i * s = i * a = q * = 0, dr/dt = 0 in eq. (6), and dc/dt = 0 in eq. (7) . thus, the dynamics always reaches the fixed point s * which is stable for all considered parameters. it is known that for systems composed of differential equations with r unknown parameters, 2r + 1 experiments with real data are needed to obtain all the information that is potentially available about the parameters [37] . since in our case we have only two adjustable parameters (r = 2), we need at least 5 real data to adjust parameters correctly. this minimum value is automatically taken into account in all numerical simulations when adjusting the parameters. empty circles in fig. 3 are the real data for the cumulative number of confirmed cases of covid-19 for the four countries analyzed. to find the best values for the pairs (θ, κ s ) = (θ ef f , κ ef f s ) that fit the real data and the best time-series split in periods p i , we performed simulations varying θ ∈ [0.5, 5.0] using a step equal to 0.1 and κ s ∈ [0.0, 1.0] using a step equal to 0.05 and testing different combinations of periods p i , always obeying the minimum amount of real data requested in each period. the goal of these simulations is to minimize the mean square error between the numerical results and real data. thereon, we need five pairs of parameters in fig. 3 (a), namely p 1 , p 2 , p 3 , p 4 , and p 5 for belgium, and six pairs of parameters for the other countries, seen in fig. 3 (b)-3(d). details of the adjustable parameters are given in table 2 . the initial condition e(t 0 ) for the variable e(t) is determined inside the first period p 1 of the data considering the interval e(t 0 ) ∈ [c(t 0 )/5, 10c(t 0 )] using a step equal c(t 0 )/5, where c(t 0 ) is the cumulative number of confirmed cases obtained from the who data for the first day in p 1 . we do not start the parameter adjustment from the first day of reported infections, but later on. the model produces better results in such cases. after adjusting the parameters to the real data, the black-continuous curves in fig. 3 display the results of integrating equations of the model. we observe that these curves nicely reproduce the data in all cases. when real data are not available anymore, the black-continuous curves represent projections of the cumulative number of infected individuals until the day 150, considering that the pair (θ ef f , κ ef f s ) found in the last period will not be changed. in this section, we discuss the effects of distinct strategies applied in different days on the total number of infected individuals. essentially we discuss two strategies: (i) vary the degree of the social distance; (ii) for a constant value of the social distance, vary the number of daily tests that allow identifying and isolating the infected asymptomatic individuals. as mentioned before, fig. 3 displays the real data (empty circles) and black-continuous curves, which were adjusted to fit the data. the results are shown for belgium in fig. 3(a) , brazil in fig. 3(b) , uk in fig. 3(c) , and usa in fig. 3(d) . during the integration of the odes of the model, it is possible to change the parameter θ, which represents the amount of social distance. therefore, we changed this parameter from 0.5 to 2.5 using a step of 0.002 in three distinct dates, namely april 16 th (greendashed curves), april 30 th (blue-dashed curves), and may 14 th (red-dashed curves). curves with dark colors are related to θ = 2.5, and light colors to θ = 0.5. worth mention that high values of θ mean low degrees of social distance, what can potentialize the epidemic spread. we see, in the case of belgium, for example, that strong social distance strategies (θ = 0.5) can flatten the curves for the three distinct days. however, their efficiency in flattening the curves becomes less for later days (see blue and red light dashed curves). on the other hand, if social distance strategies are relaxed to θ = 2.5 in belgium when compared to θ ef f = 0.7 obtained for the last period p 5 (see table 2 ), the number of infected people increases very much. furthermore, if you wait longer to relax the social distance, days april 30 th (blue-dashed curves) or may 14 th (reddashed curves), for example, the total number of infected cases diminishes. essentially the same behavior is observed for all the other countries analyzed. please see figs. 3 in all these simulations the values κ s = 1.0 and κ a = 0 were kept fixed. at next, we keep the social distance parameter constant at θ = 2.0, set κ s = 1.0, and change the daily rate of identification of asymptomatic infected individuals. the choice for this strategy is that without tests it is impossible to recognize that asymptomatic individuals are infected. in the simulations, we varied κ a from 0.1 to 1.0 using a step of 0.009. results are presented in fig. 4 for the same countries from fig. 3 . for better visualization, we start the plot at later times when compared to fig. 3. figures 4(a) , 4(c), 4(e), and 4(g) display the total cumulative number of confirmed infected cases and figs. 4(b), 4(d), 4(f), and 4(h) show the cumulative number of only symptomatic infected individuals. strategies are again applied in days april 16 th (green-dashed curves), april 30 th (bluedashed curves), and may 14 th (red-dashed curves). curves with dark colors are related to κ a = 1.0 and curves with light colors to κ a = 0.1. this constant can be interpreted as follows: κ a = 0.1, for example, represents a daily rate of identification and isolation of 10% of all asymptomatic infected individuals. this represents a huge number of daily tests for countries like brazil and usa, which have a large population. to make it possible to compare the projection tendencies, for which κ a = 0, and the scenarios shown in fig. 4 , we compute the cumulative number of symptomatic infectious cases (b). in this quantity, asymptomatic cases or those with mild symptoms are not considered. similar to the c variable, b is an auxiliary variable of the model, obtained by integrating the ode let us discuss results from fig. 4 taking just one country: uk. in fig. 4 (e) we observe that the strategy of realizing tests on asymptomatic individuals increases the total number of confirmed cases in-stantly. for the largest value κ a = 1.0 for example, the dark green curve increases very much on the day april 16 th . for κ a = 0.1, the light green curve barely changes in this day. however, after around 15 days, both curves cross each other, and the dark green curve asymptotically converges to a much smaller value than the light-green curve, which shows that the realization of a huge amount of daily tests to identify and isolate asymptomatic individuals is also an efficient strategy that could be applied to relax the social distance (increase the value of θ). nevertheless, it is important to mention that, for countries with large populations, values κ a ≈ 1.0 are not practical parameters. the same behavior can be observed when the tests are applied in days april 30 th (blue-dashed curves) and may 14 th (red-dashed curves). essentially an analogous interpretation is valid for the other countries. one difference is observed in brazil. in fig. 4(c) we can see that all the dashed curves cross the black-continuous curve of the tendency, meaning that even the late actions were able to diminish the number of infected individuals. it occurs because of the constant value θ = 2.0 is lower than the θ ef f = 2.1 obtained in the last period p 6 for brazil (see table 2 ). this is not the case for the other countries since black-continuous curves had a smaller value of θ ef f at p 6 , or p 5 for belgium (see table 2 ), when compared to θ = 2.0 used in fig. 4 . at next, we discuss some projections for the cumulative number of symptomatic infected individuals, shown in figs. 4(b) for belgium, 4(d) for brazil, 4(f) for uk, and 4(h) for usa. now, we take the example of the usa. when increasing the value of θ from θ ef f = 1.10 (see table 2 ) to θ = 2.0 and setting κ a = 1.0, on april 16 th , the dark green curve tends to flatten the growth of the cumulative number of symptomatic infected cases. on the other hand, for κ a = 0.1, the tendency is to increase such quantity when compared to the blackcontinuous curve. this projects bad news for the usa in case they relax the social distance (increase the value of θ) and apply a small number of tests to the identification of asymptomatic infected individuals. similar behavior is observed for the other countries. the only difference is for brazil, shown in fig. 4(d) , where the black-continuous curve is lying above the dashed curves once the value of θ used in these strategies is lower than the θ ef f obtained in p 6 for brazil. the projections tend to get worst as the application day of the strategy is delayed. the cumulative number of confirmed cases of covid-19 until april 30 th , 2020, is demonstrated for four exemplary countries: belgium, brazil, uk, and usa, representing three distinct continents. after an initial period with a low incidence of newly infected people, a power-law growth of the number of confirmed cases is observed. for each country, we found a distinct growth exponent. usa leads the increasing rate, followed by uk, brazil, and belgium. for belgium, uk, and usa, countries with a large number of infected individuals, the power-law growth gave place to a distinct behavior when approaching saturation. brazil is still in the power-law regime. such updates of the data and projections corroborate recent results regarding the power-law growth of the cumulative number of infected individuals by the new coronavirus and its strong correlation between different countries around the world [12] . furthermore, we study a variation of the well known seir epidemic model [16, 38] for predictions using (or not) distinct government strategies applied on three distinct dates, namely april 16 th (early action), april 30 th (current action), and may 14 th (late action). the main goal is to show that time is one of the most important weapons we have in the battle against the covid-19. recently, it has been shown that there is a short time window for which it is possible to avoid the spread of the epidemic [39] . in this work, the authors applied the richards growth model to study the fatality curves of some countries. their findings show that, in general, the efficiency of an intervention strategy decays quickly as the adoption time is delayed, corroborating that time is essential in containing an outbreak. in our case, in the three days mentioned above, we applied two strategies: (i) distinct degrees of social distance (vary θ), and (ii) distinct degrees of identification of asymptomatic individuals (vary κ a ). in the first strategy, we change the values of θ from 0.5 to 2.5, meaning strong and essentially no social distance containments, respectively. in the second strategy, we change κ a from 0.1 to 1.0. this can be interpreted as identifying daily 10% of all asymptomatic individuals when κ a = 0.1. the ideal case is represented using κ a = 1.0, when all asymptomatic infected people are identified each day. results for all countries convince us that nonpharmacological strategies must be applied as soon as possible. these include social distance and a large number of testing and immediate isolation of asymptomatic infected individuals. furthermore, time delays in applying such strategies lead to an irreversible catastrophic number of infected people. and they also acknowledge computational support from prof. c. m. de carvalho at lftc-dfis-ufpr (brazil). c. m. also thanks fapesc (brazilian agency) for financial support coronavirus: why you must act now power-law distribution in the number of confirmed covid-19 cases a mathematical model for the spatiotemporal epidemic spreading of covid19, medrxiv essai d'une nouvelle analyse de la mortalite causee par la petite verole et des avantages de l'inoculation pour la prevenir daniel bernoulli's epidemiological model revisited a contribution to the mathematical theory of epidemics a delayed sir epidemic model with general incidence rate an agent-based modeling for pandemic influenza in egypt modeling influenza epidemics and pandemics: insights into the future of swine flu (h1n1) transmission dynamics and control of severe acute respiratory syndrome strong correlations between powerlaw growth of covid-19 in four continents and the inefficiency of soft quarantine strategies effective containment explains sub-exponential growth in confirmed cases of recent covid-19 outbreak in mainland china quantitative assessment of the role of undocumented infection in the 2019 novel coronavirus (covid-19) pandemic effects of quarantine in six endemic models for infectious diseases nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study implications of heterogeneous sir models for analyses of covid-19 modeling the dynamics of viral infections in presence of latently infected cells the approved dose of ivermectin alone is not the ideal dose for the treatment of covid-19 transition from endemic behavior to eradication of malaria due to combined drug therapies: an agent-model approach polynomial growth in branching processes with diverging reproductive number the mathematics of infectious diseases verhulst and the logistic equation (1838), in: a short history of mathematical population dynamics small worlds: the dynamics of networks between order and randomness the physics of foraging: an introduction to random searches and biological encounters the covid-19 pandemic: growth patterns, power law scaling, and saturation data-driven modeling reveals a universal dynamic underlying the covid-19 pandemic under social distancing, medrxiv graph theory suggests covid-19 might be a 'small world' after all fractal kinetics of covid-19 pandemic measuring and testing dependence by correlation of distances the distance correlation ttest of independence in high dimension distance correlation detecting lyapunov instabilities, noise-induced escape times and mixing decay of the distance autocorrelation and lyapunov exponents early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia modeling and dynamics of infectious diseases (series in contemporary applied mathematics) stability of the endemic equilibrium in epidemic models with subpopulations for differential equations with r parameters, 2r + 1 experiments are enough for identification global dynamics of a seir model with varying total population size modelling fatality curves of covid-19 and the effectiveness of intervention strategies the authors thank cnpq (brazil) for financial support (grant numbers 432029/2016-8, 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.author contributions e.l.b. contributed to the model implementation. r.m.s. and c.m. collected and analyzed the data, and m.w.b. mainly wrote the paper. all authors contributed to the discussion and analysis of the results and the final compilation of the work. key: cord-309875-8awkpi2p authors: cavalcante, francisco pimentel; novita, guilherme garcia; millen, eduardo camargo; zerwes, felipe pereira; de oliveira, vilmar marques; sousa, ana luiza lima; junior, ruffo freitas title: breast cancer and covid‐19 pandemic in brazil date: 2020-08-05 journal: j surg oncol doi: 10.1002/jso.26143 sha: doc_id: 309875 cord_uid: 8awkpi2p nan after the pandemic outbreak, for reasons well described in this review, many emergency guidelines [2] [3] [4] were developed by experts from around the world. they suggested postponing surgery for invasive ebc, recommending strategies according to molecular subtype. for example, for tumors that express hormone receptors (hr+), the recommendation could be to start treatment with neoadjuvant endocrine therapy (net) for 3 to 6 months, while in adverse biologic subtypes, such as her2+ and triple-negative (tn), the recommendation could be to extend the use of neoadjuvant chemotherapy (nact). in addition, there was a recommendation to avoid the major procedure, such as the use of myocutaneous flaps in breast reconstruction and prophylactic operations. although some of these suggestions have not been officially endorsed by the brazilian society of mastology (sbm), it is possible that these international guidelines had an impact in brazil. to assess this hypothesis, during the months of april and may 2020, an electronic survey was conducted among sbm members regarding the initial management of ebc. we created questions regarding invasive, t1/2 n0 hr+, and t1n0 her2+/tn cancers, because these patients, in brazil, are normally submitted to primary surgery. after approval of the sbm's internal review board, the questionnaire was sent to 1462 brazilian mastologists. the results were submitted to a scientific journal, but we have an online "preprint" publication of the study data. 5 there were 503 responders these findings highlight important changes in the approach of the mastologists at the beginning and during the pandemic, particularly with respect to hr-positive tumors, and reflects, in our opinion, the disagreements between the emergency guidelines described by garg et al. 1 however, since the data were developed from a survey, we cannot confirm that these recommendations translated into treatment recommendations for actual patients. more studies are needed to know the real impact of the pandemic on patients treated with breast cancer in the pandemic period. discordance of covid-19 guidelines for patients with cancer: a systematic review a practical approach to the management of cancer patients during the novel coronavirus disease 2019 (covid-19) pandemic: an international collaborative group recommendations for prioritization, treatment, and triage of breast cancer patients during the covid-19 pandemic. the covid-19 pandemic breast cancer consortium recommendations for triage, prioritization and treatment of breast cancer patients during the covid-19 pandemic management of early breast cancer during the covid-19 pandemic in brazil the authors declare that there are no conflict of interests. key: cord-286130-4f7otdx1 authors: xavier, joilson; giovanetti, marta; adelino, talita; fonseca, vagner; barbosa da costa, alana vitor; ribeiro, adriana aparecida; felicio, katlin nascimento; duarte, clara guerra; ferreira silva, marcos vinicius; salgado, álvaro; lima, mauricio teixeira; de jesus, ronaldo; fabri, allison; soares zoboli, cristiane franco; souza santos, thales gutemberg; iani, felipe; ciccozzi, massimo; bispo de filippis, ana maria; teixeira de siqueira, marilda agudo mendonça; de abreu, andré luiz; de azevedo, vasco; ramalho, dario brock; campelo de albuquerque, carlos f.; de oliveira, tulio; holmes, edward c.; lourenço, josé; junior alcantara, luiz carlos; assunção oliveira, marluce aparecida title: the ongoing covid-19 epidemic in minas gerais, brazil: insights from epidemiological data and sars-cov-2 whole genome sequencing date: 2020-08-11 journal: emerging microbes & infections doi: 10.1080/22221751.2020.1803146 sha: doc_id: 286130 cord_uid: 4f7otdx1 the recent emergence of a coronavirus (sars-cov-2), first identified in the chinese city of wuhan in december 2019, has had major public health and economic consequences. although 61,888 confirmed cases were reported in brazil by 28 april 2020, little is known about the sars-cov-2 epidemic in this country. to better understand the recent epidemic in the second most populous state in southeast brazil minas gerais (mg) we sequenced 40 complete sars-cov-2 genomes from mg cases and examined epidemiological data from three brazilian states. both the genome analyses and the geographical distribution of reported cases indicate for multiple independent introductions into mg. epidemiological estimates of the reproductive number (r) using different data sources and theoretical assumptions suggest the potential for sustained virus transmission despite a reduction in r from the first reported case to the end of april 2020. the estimated date of sars-cov-2 introduction into brazil was consistent with epidemiological data from the first case of a returned traveller from lombardy, italy. these findings highlight the nature of the covid-19 epidemic in mg and reinforce the need for real-time and continued genomic surveillance strategies to better understand and prepare for the epidemic spread of emerging viral pathogens.. the world health organization (who) office in china was informed about a cluster of new cases of pneumonia of unknown aetiology in the city of wuhan (hubei province), in late december 2019 [1] . shortly afterwards, a new type of coronavirus, now termed sars-cov-2, was isolated and identified by chinese authorities, with its genetic sequence shared with the international community on 10 january 2020 [2] [3] [4] [5] . phylogenetic analysis revealed that sars-cov-2 was similar to other (epidemic) betacoronaviruses, such as severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov) [4, 5] , and was clearly related to coronaviruses isolated from bats and malayan pangolins (manis javanica) indicative of a zoonotic origin [2, [5] [6] [7] . to date, more than 10.7 million cases of the disease caused by sars-cov-2, termed covid-19, have been reported globally [8, 9] . on 11 march 2020, the who declared a pandemic, prompting a dramatic increase in international concern and response [10] . on 26 february 2020, the first confirmed case of covid-19 was reported in são paulo (sp) state, brazil [11] . two months later (28 april 2020), 61,888 cases and 4,205 deaths attributed to covid-19 had been reported in brazil [12] . initial phylogenetic analysis using the first two sars-cov-2 complete genomes isolated in são paulo from travellers returning from italy revealed two independent introductions into the country relative to the data set available at that time [13] . the state of minas gerais (mg) is the second largest brazilian state in terms of population size, estimated at approximately 21 million people [14] . due to its large population size and strong connections to active neighbouring states such as são paulo and rio de janeiro, the state of mg is likely to be highly affected by the covid-19 pandemic. genetic analyses and surveillance allow the characterization of circulating viral lineages, the inference of introduction events and the reconstruction of transmission patterns [15] . together with epidemiological data they constitute powerful tools to assist public health initiatives and preparedness. herein, we present a summary of epidemiological data and the generation and analysis of 40 new sars-cov-2 genome sequences isolated from clinical samples of confirmed cases from mg. our aim was to provide a preliminary epidemiological overview of sars-cov-2 circulation and introduction events into minas gerais. anonymised samples processed in this study were sent to the central public health laboratory/octávio magalhães institute (iom) of the ezequiel dias foundation (funed), which belongs to public laboratories network from the brazilian ministry of health (bmoh). they were previously obtained by the local health services for the routine diagnosis and epidemiological surveillance of sars-cov-2. the availability of these samples for research purposes during outbreaks of international concern is allowed under the terms of the 510/2016 resolution of the national ethical committee for research -brazilian ministry of health (conep -comissão nacional de ética em pesquisa, ministério da saúde): this authorizes the use of clinical samples collected in the brazilian central public health laboratories to accelerate knowledge building and contribute to surveillance and outbreak response. the study protocol was reviewed and approved by research ethics committee of the universidade federal de minas gerais with approval no. 32912820.6.1001.5149. samples used in this study were from residual anonymised clinical samples, with no or minimal risk to patients, provided for research and surveillance purposes as described above. swab samples collected from covid-19 suspected cases were collected throughout the state of mg and sent to iom-funed facilities. at the iom-funed facilities they were submitted to total rna extraction with an automated protocol on the qiasymphony platform using the dsp virus/pathogen kit (qiagen), following the manufacturer's recommendations. the molecular diagnosis was performed on a 7500 real-time pcr system (thermofisher scientific), using a rt-qpcr singleplex kit for the sars-cov-2 envelope and rnadependent rna polymerase genes developed by bio-manguinhos/fiocruz (rio de janeiro, brazil) and provided by the brazilian ministry of health, following the manufacturer's recommendations. we selected 48 samples with rt-qpcr positive results, collected up to 3 april 2020 from patients residing in different municipalities of the state of mg and presenting with symptoms such as fever, cough, headache, dyspnea, sore throat and/or vomiting. samples were selected based on cycle threshold (ct) values ≤ 32. associated epidemiological data, such as symptoms, travel history and municipality of residency, were collected from medical records accompanying the collected samples provided by iom/funed. for cdna synthesis, the superscript iv reverse transcriptase kit (invitrogen) was used following the manufacturer's instructions. the generated cdna was subjected to multiplex pcr sequencing using q5 high fidelity hot-start dna polymerase (new england biolabs) and a set of specific primers designed by the artic network (https://github.com/articnetwork/artic-ncov2019/tree/master/primer_schemes/ ncov-2019/v1) for sequencing the complete sars-cov-2 genome [16] . pcr conditions have been previously reported in [16] . all experiments were performed in biosafety level-2 cabinet. amplified pcr products were purified using the 1x ampure xp beads (beckman coulter) following previously a published protocol [17] . purified pcr products were quantified using the qubit® dsdna hs assay kits (invitrogen), following the manufacturer's instructions. of the 48 samples, only 40 contained sufficient dna (≥ 2ng/µl) to proceed to library preparation. sequencing libraries were prepared using the oxford nanopore ligation sequencing kit (sqk-lsk109) following previously a published protocol [17] . before pooling all samples, each sample was barcoded using the native barcoding expansion kits (nbd104 and exp-nbd114). after barcoding adaptor ligation, sequencing libraries were loaded on a flow cell (flo-min106) for subsequent minion sequencing, programmed to run for six hours. reads were basecalled using guppy and barcode demultiplexing was performed using qcat. consensus sequences were generated by de novo assembling using genome detective and coronavirus typing tool [18, 19] . public sars-cov-2 complete genome sequences available up to 15 april 2020 were retrieved from the gisaid database (https://www.gisaid.org/). sequences were aligned using mafft (ff-ns-2 algorithm) employing default parameters [20] . the alignment was manually curated to remove artefacts at the terminal regions and within the alignment using aliview [21] . phylogenetic analysis of these sequences was performed using the maximum likelihood method implemented in iq-tree (version 1.6.10), employing the best-fit model of nucleotide substitution according to the bayesian information criterion (bic) as indicated by the model finder application implemented in iq-tree [22] . the statistical robustness of individual nodes was determined using 1000 bootstrap replicates. lineage assessment was conducted using the phylogenetic assignment of named global outbreak lineages tool available at https://github.com/hcov-2019/ pangolin [23] . four data sets of complete or near-complete sars-cov-2 genome sequences were generated. data set 1 (n = 3,102) comprised the data reported in this study (n = 40) plus publicly available sars-cov-2 sequences (n = 3,062) from gisaid. subsequently, to investigate the evolutionary behaviour of sars-cov-2 within the three different sars-cov-2 lineages (a, b and b.1), bayesian molecular clock analysis was conducted on three smaller subsets of data for each of the three lineages identified in the ml phylogeny and containing isolates from mg (data set 2 for subset a n = 100; data set 3 for subset b n = 84; data set 4 for subset b.1 n = 169). ml trees from these three data subsets were inspected in tempest v1.5.3 for the presence of a temporal (i.e. molecular clock) signal [24] . linear regression of root-to-tip genetic distances against sampling dates indicated that the sars-cov-2 sequences evolve in a relatively-strong clock-like manner (r = 0·43; r = 0·47; r = 0·40 from subset a; b and b.1, respectively) (supplementary figure s18 ). for more detailed bayesian time-scaled phylogenetic analysis we employed the beast 1.10.4 program [25] . for this analysis we employed the strict molecular clock model, the hky+γ4 codon partitioned (cp)1 + 2,3 nucleotide substitution model and the exponential growth coalescent model [26] . we computed mcmc (markov chain monte carlo) triplicate runs of 100 million states each, sampling every 10.000 steps for each data set. convergence of mcmc chains was checked using tracer v.1.7.1 [27] . maximum clade credibility trees were summarized from the mcmc samples using treeannotator after discarding 10% as burn-in. data used in the epidemiological analysis were retrieved from https://github.com/wcota/covid19br [28] . after the who declared the outbreak of sars-cov-2 a public health emergency of international concern (pheic) on 30 january 2020, the brazilian government declared a public health emergency of national importance on 3 february 2020, enabling the introduction of measures to prevent and control virus spread [29] . twenty-three days later, the first confirmed case in brazil was reported in the city of são paulo, related to a traveller returning from lombardy, italy ( figure 1 ) [11] . by the 28th april 2020, more than 61,888 covid-19 cases were confirmed in brazil, 1,578 of which were from mg ( figure 2a ) [30] . over this period, mg registered 71 covid-19-related deaths and the capital city, belo horizonte, with an estimated population of 2.5 million people, reported 555 cases [30, 31] . figure 2a shows mg's epidemic (reported cases) curve compared to those of two other neighbouring states, são paulo (sp) and rio de janeiro (rj). temporal trends reveal a growth in the number of cases in mg, although with sp accounting for the largest number of cases and deaths (24,041 cases; 2,049 deaths) by covid-19 up to 28th april 2020. epidemiological analyses using cases and mortality time series data from three brazilian states without access to the total number of tests in time and in each state, we obtained a crude estimate of the case fatality ratio (cfr) for mg, sp and rj as the ratio between the number of reported deaths and cases [32] . accordingly, cfr was found to increase with time in all states (supplementary figure s2 ), with means from date of first reported case up to the 28 april in each state as 2.67% for mg, 5.39% for rj and 6.0% for sp. although all such comparisons should be made with caution, the cfr in sp and rj was consistently higher than reported in other localities; for example, 2.6% (95% ci 0·89-6·7) for the diamond princess cruise ship [33] , and 3.67% (95% ci 3.56-3.80) and 1.2% (95% ci 0.3-2.7) and 1.4% (95% ci 0.9-2.1) for different chinese regions [33] [34] [35] . we used the mortality time series (mts) from mg, sp and rj to project the (unobserved total) cumulative number of infections, making two main simplifying assumptions: first, that the infection fatality ratio (ifr) of sars-cov-2 would be similar in the brazilian states to that reported elsewhere; and second, that the number of cumulative deaths in each state were well reported. we utilised the ifr estimated by verity and colleagues (0.66%, ci 95% 0.39-1.33% [34] ), for its general use in the modelling literature [36] . the cumulative number of infections in time was is the number of reported cases in time. we found that the observation rate decreased in time for all states, a likely outcome of epidemic growth superseding tracing and testing efforts as the epidemic progressed (supplementary figure s1 ). by 28 april 2020, the last time point analysed, rj and sp had similar observation rates at 7.6% and 7.74% (respectively), while in mg, where the epidemic started later, the observation rate was 15.3% (i.e. 1 reported case in 7 infections). to compare transmission potential, we used reported cases (cts) and mortality time series (mts) from mg, sp and rj states to estimate the (effective) reproduction number, r . for this, we performed maximum likelihood estimation of the (cts and mts) epidemic growth r using a phenomenological model, and two theoretical formulations on how r relates to r -one based on the seir epidemiological framework by wallinga and colleagues [37] , and another on the distribution of the serial interval [36] using geographic information from reported data in each state ( figure 2c ), we found cases and deaths to be disproportionally reported in capital cities for the rj and sp states but not for mg (supplementary figures s13-14) . typically, incidence (cases, deaths) are normalized per 100k individuals, taking into account the total population size of each state. because of the very different spatial dispersion of cases and deaths in mg when compared to sp and rj, we also calculated the effective population size; that is, the sum of the population sizes of all municipalities with reports. when using reported cases, we found that the effective population sizes were ∼100%, ∼100% and 64% of the total population sizes of rj, sp and mg, respectively. when using reported deaths, the effective population sizes were ∼95%, ∼92%, and 35% of the total population sizes of rj, sp and mg, respectively. overall these numbers suggest that in mg cases and deaths have been reported only in a subset of the overall population, while in the other states sars-cov-2 appears widely dispersed. incidence of reported cases per 100k using the effective population size was ∼60 in sp, ∼51 in rj and ∼7.85 in mg (supplementary figure figure 1 . timeline of key events following the first confirmed case of covid-19 in brazil. events below the line occurred in minas gerais (mg) state, while national events are presented above the line. codes in parentheses refer to the identification code (cv#) of the isolates from the cases described in this study. s7), while incidence of deaths per 100k was ∼5.56 in sp, ∼4.69 in rj and ∼0.94 in mg (supplementary figure s12 ). in mg, samples from (clinically) suspected cases were screened at the central public health laboratory/octávio magalhães institute (iom) of the ezequiel dias foundation (funed), which belongs to the public laboratories network of the brazilian ministry of health (moh). by 3rd april 2020, iom/funed had performed 3,303 rt-qpcr tests for sars-cov-2 on swab samples from suspected cases. we used nanopore sequencing to generate complete genomes from 40 covid-19 patients in 15 different municipalities in mg (table 1) . of the 40 samples, 17 (42.5%) were from the state's capital (belo horizonte), while the other municipalities were represented by one or a maximum of three samples. these samples were from 17 females and 23 males, with collection dates ranging from 4 march 2020 to 26 march 2020 ( table 1 ). the median age of the patients was 35 years (ranging from 19-79 years old). the first sample that tested positive by rt-qpcr at iom/funed was collected on 4th march 2020 (table 1 and figure 1 ). selected samples had cycle threshold (ct) values that ranged from 16.41 to 31.86 (median=22.945). we found no demographic variables (age, gender) to be statistically correlated with sample ct (supplementary figure s17 ). the new sequences had a median genome coverage of 82.5% related to the reference genome nc_045512.3 (s1 table) . all sequences generated in this study have been submitted to the gisaid following who guidelines [38] . of the 17 (42.5%, n=40) sequenced cases with available travel history information, 14 (82.35%, n=17) reported international travel while three reported domestic travel (table 1) . two among the later visited the city of são paulo and one the city of rio de janeiro. of the international travel-related cases, seven (50%) were linked to travel to european countries (portugal, spain, italy, switzerland, austria, england, belgium, germany, czech republic, and hungary), while six reported travel to countries in the americas (usa, colombia, jamaica, cayman islands, panama, chile, and peru). one case reported travel to israel. to explore the epidemiological history of the virus in mg, we performed a maximum likelihood (ml) phylogenetic analysis on the 40 new sequences combined with another 3,062 sequences deposited in gisaid up to 15 april 2020. we also made use of a publicly available tool for the automated lineage assignment within sars-cov-2 (https://github.com/hcov-2019/pangolin) [23] . our estimated phylogeny identified two major clades branching at the root of the tree (figure 3 ). these two clades were named lineages a and b, following a recently proposed sars-cov-2 lineage nomenclature [39] : lineage a can be defined by the wuhan/wh04/2020 sequence, while lineage b is represented by wuhan-hu-1. lineage b can be further divided into a number of component sublineages, and our phylogenetic analysis revealed that the majority (n=37, 92.5%) of mg sequences belonged to lineage b.1 which contains sequences from a variety of countries including australia, china, canada, malaysia, and the usa [40] (figure 3 , table 1 ). of these 37 b.1 sequences, 11 were isolates from cases that reported travel to european countries (cv2, cv3, cv11, cv13, cv17) or the americas (cv4, cv6, cv12, cv20, cv28, cv35), in addition to the isolate cv1 from a traveller who returned from israel. aside from sublineage b.1, two sequences were assigned to lineage b in our ml phylogeny (isolates cv22 and cv36, with the former reporting travel to germany), while one sequence could be assigned to lineage a (isolate cv7) who reported travel to european countries (full results from the pangolin covid-19 lineage assigner are presented in supplementary table s2 ). to assess the evolution of these lineages in more detail and in time, we performed bayesian timemeasured phylogenetic analysis using a molecular clock model. we analysed three subsets of data (a, b, b.1) extracted from each lineage from the ml tree that included brazilian sequences. our maximum clade credibility (mcc) trees showed that most of mg's sequences were interspersed with viruses sampled from other countries (figure 4b, c, d) . this pattern, similar to that observed elsewhere [40] [41] [42] , is also in accordance with our ml tree and with the epidemiological data, indicating that the appearance of these viruses were linked to travel exposure rather than community transmission, and reinforcing the idea that multiple independent introductions from overseas occurred in mg. in contrast, some other sars-cov-2 sequences from mg grouped together, forming clusters that included sequences from brazil and other countries: these are apparent in the data subset b.1 phylogeny (figure 4d ). however, these clusters have very low posterior probability support, likely due to the low genetic diversity of sars-cov-2 genomes [43] [44] [45] . nonetheless, four clusters, each comprising only two mg sequences, showed posterior probabilities >80%. one of these clusters (figure 4d) , with a posterior probability of 100%, was formed by isolates cv34 and cv36 that arose from local contacts with a confirmed and a suspected covid-19 case, respectively. from the time-scaled phylogenies, we estimated the mean time of the most recent common ancestor (tmrca) of the sars-cov-2 epidemic in brazil to range from 27 january to 22 february 2020 (95% hpd interval; mean date of 10 february 2020). this is consistent with the start of reported cases in brazil and with the epidemiological data from the first case confirmed in sp, regarding a traveller returning from lombardy, italy, on 21 february 2020 [11, 13] . we provide a preliminary characterization of the ongoing covid-19 epidemic in mg, the second largest state in brazil with respect to population size, where 1,578 cases were reported up to 28 april 2020. we report genomic data obtained by sequencing 40 sars-cov-2 infection cases confirmed by rt-qpcr in mg. we also collected epidemic data of case and death time series to estimate key epidemiological metrics such as the case fatality ratio, the observation rate and the effective reproduction number, r. combined epidemiological and genomic data strongly suggest that the epidemic of sars-cov-2 infection in mg was associated with multiple independent importations from returned travellers. epidemiological analysis using case and death time series revealed that in mg, where case incidence was ∼7.85, the distribution of cases and deaths was more spatially uniform (i.e. less focused on belo horizonte), while in sp and rj states it was more centralized around capital cities, although with a wide variance. the estimated observation rate was 15.3% in mg, indicating that 1 case in 7 was reported in that state by 28 april 2020. despite the different approaches used, the r values estimated for mg were similar to those estimated previously [46] . as all estimates of r were > 1, we conclude that virus transmission is not controlled and that the epidemic in mg will continue to grow unless stricter non-pharmaceutical interventions are implemented. our time-measured phylogeny revealed that mg's isolates are scattered throughout the tree, although some clusters suggestive of local transmission were also observed. this dispersed distribution has been observed in other studies such as from china [42] and new york [47] , and is consistent with the selfdeclared travel history of patients to different countries in the americas and europe. from our phylogeny we inferred that multiple independent importations of sars-cov-2 infection from returned travellers had occurred in mg. this is noteworthy because it has been argued that several introductions are necessary for an outbreak to establish in a new location [48] . the mean time of the most recent common ancestor of all brazilian strains analysed in this study was estimated to be from 27 january to 22 february 2020, and range that includes the first covid-19 confirmed case reported in 21 february 2020 [49] . these results illustrate that by combining genomic data and available epidemiological information we can generate more reliable phylogenetic inferences. despite the grouping of some mg sequences, because of the small sample size data which covers only about 30 days of the mg epidemic we cannot infer a close relationship between these sequences with certainty at this stage. in addition, the low genetic diversity of sequences available limits conclusions about sars-cov-2 directionality and spread based on genetic data alone. as noted elsewhere [43] , such phylogenetic results should be approached with caution and considered as hypothesis-generating with respect to the transmission events of sars-cov-2 in a local setting. in conclusion, at the end of april 2020, the covid-19 epidemic in the state of mg was expanding (r>1) and highly geographically dispersed, with many cases and deaths reported away from the capital city. genomic data and other epidemiological information from travel-related cases allowed us to identify several independent introductions in mg, helping to explain the geographical patchiness of reported cases and deaths. these initial insights based on the restricted data reveal that transmission is likely to continue in the near future and suggest there is considerable room to improve reporting. increasing covid-19 testing and sars-cov-2 genomic sequencing will undoubtedly help to understand how the virus is spreading in brazil and thus greatly assist epidemic control. novel coronavirus (2019-ncov) situation report -1 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 novel coronavirus from patients with pneumonia in china a pneumonia outbreak associated with a new coronavirus of probable bat origin pangolin homology associated with 2019-ncov the proximal origin of sars-cov-2 coronavirus disease (covid-19) situation report-165 the species severe acute respiratory syndrome-related coronavirus: classifying 2019-ncov and naming it sars-cov-2 coronavirus disease 2019 (covid-19) boletim epidemiológico especial-14 / se 18-26 de abril de coronavirus disease (covid-19) situation report -103 first cases of coronavirus disease (covid-19) in brazil, south america (2 genomes instituto brasileiro de geografia e estatística -ibge. cidades e estados: minas gerais towards a genomics-informed, real-time, global pathogen surveillance system ncov-2019 sequencing protocol. protocols.io multiplex pcr method for minion and illumina sequencing of zika and other virus genomes directly from clinical samples genome detective coronavirus typing tool for rapid identification and characterization of novel coronavirus genomes genome detective: an automated system for virus identification from high-throughput sequencing data mafft online service: multiple sequence alignment, interactive sequence choice and visualization aliview: a fast and lightweight alignment viewer and editor for large data sets iq-tree: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies phylogenetic assignment of named global outbreak lineages exploring the temporal structure of heterochronous sequences using tempest (formerly path-o-gen) bayesian phylogenetic and phylodynamic data integration using beast 1.10 sampling theory for neutral alleles in a varying environment posterior summarization in bayesian phylogenetics using tracer 1.7 confirmed cases and deaths of covid-19 in brazil, at municipal (city) level boletim epidemiológico covid-19: doença causada pelo coronavírus -19 28 de abril de 2020 estimating case fatality rates of covid-19 estimating the infection and case fatality ratio for coronavirus disease (covid-19) using age-adjusted data from the outbreak on the diamond princess cruise ship estimates of the severity of coronavirus disease 2019: a model-based analysis estimating clinical severity of covid-19 from the transmission dynamics in wuhan, china estimating the number of infections and the impact of non-pharmaceutical interventions on covid-19 in 11 european countries how generation intervals shape the relationship between growth rates and reproductive numbers data sharing during the novel coronavirus public health emergency of international concern. bull world health organ a dynamic nomenclature proposal for sars-cov-2 to assist genomic epidemiology genomic epidemiology of novel coronavirus -global subsampling rapid sars-cov-2 whole genome sequencing for informed public health decision making in the netherlands genomic epidemiology of sars-cov-2 in guangdong province a snapshot of sars-cov-2 genome availability up to april 2020 and its implications (preprint) regaining perspective on sars-cov-2 molecular tracing and its implications. medrxiv phylodynamic analysis | 176 genomes | 6 report 21: estimating covid-19 cases and reproduction number in brazil. medrxiv introductions and early spread of sars-cov-2 in the new york city area. medrxiv early dynamics of transmission and control of covid-19: a mathematical modelling study importation and early local transmission of covid-19 in brazil we thank all the authors, originating and submitting laboratories that have kindly deposited and shared genome data on gisaid epicov database, on which this research is based. an acknowledgment table can be found in supplementary table s3 . we thank all personnel from health surveillance system from the state of mg that assisted with epidemiological data collection. we are also grateful for the support provided by the personnel from the central public health laboratory/octávio magalhães institute (iom) of the ezequiel dias foundation (funed). no potential conflict of interest was reported by the author(s). key: cord-315624-57kzulqv authors: storopoli, jose; mesch, gustavo s. title: confidence in social institutions, perceived vulnerability and the adoption of recommended protective behaviors in brazil during the covid-19 pandemic date: 2020-10-27 journal: soc sci med doi: 10.1016/j.socscimed.2020.113477 sha: doc_id: 315624 cord_uid: 57kzulqv the current worldwide covid19 pandemic has required the rapid and drastic adoption of social distancing and protective measures as the leading method for reducing the spread of the disease and death. the purpose of this study is to investigate the factors associated with the adoption of such measures in a large sample of the brazilian population. we relied on recreancy theory, which argues that confidence in the ability of social institutions and perceived vulnerability to the disease are central factors predicting the adoption of these behaviors. our results, drawn from 7,554 respondents, indicate that self-confidence in the ability to carry out these behaviors, confidence in the ability of social institutions such as the government, hospitals, health workers and the media to cope with the pandemic crisis, and risk perceptions are associated with the adoption of preventive behaviors. our results expand the recreancy theory and show that beyond the main effects, the effect of perceived vulnerability depends on the values of self-confidence and confidence in social institutions. the theoretical implications of the findings are discussed. in december 2019, scientists identified a novel coronavirus (covid-2019) that was associated with an outbreak of pneumonia in wuhan, china (garfin, silver and holman, 2020) . in a matter of weeks, over 100,000 cases and thousands of deaths were confirmed globally, with numbers rapidly increasing daily (who, 2020) . on january 30, 2020, the world health organization (who 2020) designated the covid-2019 outbreak a public health emergency of international concern. public health officials started working to communicate critical information to the public to allow communities, organizations and individuals to take the necessary and appropriate precautions and governments to develop plans and respond accordingly (perlman, 2020; sabat, et al., 2020) . in most developed countries, a major focus of the policy has been minimizing the transmission of the virus through the implementation of lockdowns, social distance and isolation of infected populations (sabat, et al, 2020; pasterlini, 2020; anderson, heesterbeek, klinkenberg, and hollingsworth, 2020) . the goal was to flatten the curve as much as possible, this is, inhibiting new infections to reduce the number of cases at any given time (block, et al, 2020) . these measures were expected to decrease overburdening healthcare systems, enable severe cases to be treated successfully and reduce overall mortality (arshed, meo and farooq, 2020) . the success of these measures is particularly critical in the case of covid-19 due to the countries have taken different steps to contain and delay the spread of the virus within their borders, with differing degrees of success. china, for example, appeared to have halted the exponential increase of confirmed cases of the virus by limiting the freedom of citizens to move around their cities, provinces, and the country (ding, et al., 2020) . the italian government, as of march 9th has implemented a similar strategy, placing much of the country in lockdown and preventing groups of people from congregating in public spaces, encouraging measures of social distancing homogeneously throughout the country (chiara, et al., 2020) . other countries have been slower to respond with such drastic action. the us, for example, waited more than two weeks after the first confirmed case within its borders to enact localized testing procedures (courtemanche, garuccio, pinkston and yelowitz, 2020) . the british government followed the instructions of its scientific advisors to delay the mass gatherings and the closure of schools, instead favoring a policy that looked akin to pursuing herd immunity, in which vulnerable groups are isolated, and healthier individuals are exposed to the virus to achieve large-scale immunity (fine et al. 2011; anderson, heesterbeek, klinkenberg, and hollingsworth, 2020) . in addition, measures were taken to restrict public gatherings, international travelling, use of face masks and recommendations of social distance. if measures like these are adopted, experts suggest that the deaths caused by coronavirus would drop (ferguson et al. 2020; . despite the variation in the measures and the timing across countries, adherence and implementation of protective measures is dependent on institutional and behavioral factors. as van bavel et al, (2020) had argued, slowing the viral transmission during pandemics requires significant shifts in behavior and social context influence the extent and speed of behavioral change. the j o u r n a l p r e -p r o o f purpose of this study is to assess the factors associated with these dramatic behavioral responses. following recreancy theory, elements included in this assessment are trust in social institutions, perceived vulnerability to becoming infected by the virus and perceived self-efficacy in implementing the measures (freudenberg, 1993) . brazil is an important case to study in this regard for several reasons. the first confirmed case of covid-19 in brazil was on february 26 th . as in other countries, the first confirmed case was a resident coming back from overseas (jesus et al., 2020) . the number of cases increased rapidly, and as of march 31, 5,933 reported cases and 206 deaths had been registered in brazil (croda, et al., 2020) . since then, the disease has been spreading rapidly. brazil has the fourth highest number of deaths and the second highest number of confirmed infections. according to the coronavirus website of brazilian ministry of health, there were more than 700,000 confirmed cases and almost 40,000 deaths, as of june 9, 2020. this estimation is considered low because underreporting of cases. in brazil, underreporting is due to the low rate of testing per 1 million inhabitants. additionally, there is significant delay in the reporting of test results (e . brazil declared a public health emergency in early march, just a few days after the world health organization did (croda, et al, 2020) . the president of brazil, jair bolsonaro, dismissed the danger posed by the virus, and rejected state-mandated social distancing and other measures (freitas, silva and cidade, 2020) . fake news had often dominated the discussion about the pandemic and had the potential to create a lack of trust in the media (aquino et al., 2020) . a recent study concluded that the pandemic management in brazil was dysfunctional, the health sector adopted a risk management policy through social distance to reduce contagion often at odds with the positions adopted by the president (freitas, silva and cidade, 2020) . thus, brazil's response to covid-19 has been limited by institutional paralysis driven by its president. the lack of trust in institutions has prompted some population groups to adopt the denialist discourse of the president (filho 2020) . the conflicting messages from the president and health authorities, and the declining trust in social institutions have left the population uncertain about the merits of protective measures to avoid the spread of the virus (ortega and orsini, 2020) . for this reason, brazil is a perfect case for our study, which investigates the role of confidence in social institutions and perceived vulnerability and efficacy in the adoption of recommended protective behaviors. there is limited evidence on the factors associated with behavior changes in prior pandemics in the early stages when preventive and protective measures are most necessary (bish and michie, 2010) . while some studies have investigated the role of trust in social institutions and risk perceptions on preventive behaviors, these often take place either in anticipation of an outbreak or long after its emergence (jones and salathe, 2009) . furthermore, they are not driven by a conceptual theoretical framework (bish and michie, 2010). our study is unique in that it provides a test of these hypotheses in real time, after the who declared covid-19 a worldwide pandemic, in a country where there is a conflict between the public health officials and central government recommendations. thus, we contribute to the literature by investigating the factors associated with the adoption of preventive measures in real time in a country in which the federal government has been slow to take measures and health system have issued policies inconsistent with the federal government. in doing this, we rely on recreancy theory, which argues that confidence in the ability of social institutions and perceived vulnerability to the disease are central factors predicting the j o u r n a l p r e -p r o o f adoption of protective behaviors (freudenburg, 2001; sapp and downing-matibag, 2009 ). recreancy is the concept used to describe the relationship between trust and risk. in our model the element of trust refers to the public's trust that social institutions will respond to social risks (freudenberg, 1993) . trust is central to the public's perception of the legitimacy of the actions of the social agencies that oversee implementing social policy designed to reduce risks. trust in institutions is important for individuals because the former have more resources than do individuals (freudenburg, 1993) . therefore, if they function appropriately, they can help individuals achieve their goals (khodyakov 2007) . lack of trust in how agencies manage risk can amplify public health concerns and increase public hesitancy to adopt preventive and avoidant behaviors (mccomas 2004; slovic 2000) . given that we do not know all the people engaged in the activities required in a pandemic crisis, we extend them a measure of trust that they are performing in a responsible and dependable manner until something disabuses us of this belief (freudenburg,1993; khodyakov 2007) . according to recreancy theory, the confidence that individuals have in society's institutions is based on their perceptions of two important considerations: the institution's competency to perform the tasks normally associated with it, and the institution's fiduciary responsibility in the sense that it is consciously working for the best interests of the population (freudenburg, 1993; slovic, 2000) . recreancy is evident in the extent to which systems are perceived as failing or unable to do their jobs (sapp and downing-matibag, 2009 ). in other words, the institutions are violating the trust put in them to be capable and operate in the best interests of all (slovic, j o u r n a l p r e -p r o o f 2000). at the extreme, the recreant system may be perceived to be not only negligent, but also to be working against society's best interests (sapp and downing-maribag, 2009 ). institutionally based trust is a specific response to the complexity of modern societies, which involves many interdependent transactions between social groups and across extensive distances of time and space (gilson 2003) . trust and confidence in social institutions is important as it provides the basis for the legitimate exercise of state authority. the notion of legitimacy refers to whether governments are entitled to be obeyed (robertson 1985) . the effective implementation of any public policy requires that state action be legitimate and so be accepted and acceptable (shao and hao, 2020) . such legitimacy is reflected in the extent to which citizens tolerate the interventions of public organizations, accept these organizations' decisions and cooperate to achieve the goals (rothstein 1998) . in social risk situations, such as epidemics, trust in the government to respond effectively, trust in health institutions to provide accurate information on prevention and treatment, and trust in the media to provide accurate information are important for the public to feel that their health interests will be attended to in the best manner possible (shao and hao, 2020) . public organizations build their legitimacy when they demonstrate the values and norms that underlie or are associated with trust through their organizational and managerial practices (gregory 1995; levi 1998) . social institutions such as the government and health systems may be viewed as a problem-solving system organized to improve the health of its residents and to be the main line of defense against contagions (giles, et al, 2011) . the health care system, therefore, comes under public scrutiny and is ultimately deemed to be positive or recreant (giles, et al, 2011) . in brazil, president bolsonaro has given little j o u r n a l p r e -p r o o f importance to taking measures to address the covid-19 pandemic. he is one of the few world leaders who refused to recognize the threat constituted by the virus and even encouraged his followers to disobey social distancing recommendations (aquino, et al; ortega and orsini, 2020) . for this reason, we distinguished between trust in the government's ability to fight outbreaks and trust in the hospitals' and health workers' ability. we expect that confidence in the brazilian government will be negatively associated with adopting protective measures, while confidence in the hospitals' and health workers' will be positively associated with adopting protective measures. this expectation is the result of contradictory recommendations that were provided by the national government and the health sector. another important institution is the media. during a global covid-19 pandemic, the public depends on the media to convey accurate information in order to make informed decisions regarding health protective behavior (garfin, silver and holman, 2020) . given its role in society's information flow, the mass media is uniquely positioned to analyze and inform the population of serious hazards and risks (cottle 1998; garfin, silver and holman, 2020) . thus, the media can potentially influence what the public regards as a health hazard and its assessment of how successful the government and public health institutions are in dealing with the threat (mesch, schwirian and kolobov 2013) . consequently, trust in the information provided by the media is viewed as an important influence on people's beliefs, attitudes and behavior. the acceptance of information depends on trusted sources transmitted by the media on the incidence, fatalities and coping measures depends on the extent to which we trust the quality of the information (garfin, silver and holman, 2020) . trusted media provides information to the public to promote appropriate health protective behavior and effective institutional responses. during the 2015 mers j o u r n a l p r e -p r o o f pandemic, it was found that exposure to traditional media affected the adoption of recommended protective behaviors (seo, 2019) . thus, trust in the media is expected to have a positive effect on the adoption of preventive behaviors. in addition to confidence in social institutions, another important dimension of recreancy theory is perceived vulnerability. risk is the likelihood of a hazard causing harm to individuals, groups or society at a given time and place (fitzpatrick and la gory 2011) . according to ulrich beck (1995) , modern societies have become "risk societies" in that a large amount of their organizational structure and resources are spent in calculating the risks of specific serious hazards. in turn, risk calculation leads to the development of strategies and procedures to manage or reduce those hazards. a central component of risk calculation is the perceived threat of disease (kraut, graff and mclean 2011) . people are likely to engage in disease prevention behaviors if they perceive that the pandemic's social risk is translated in a perception that they are highly susceptible to the disease and that the disease has severe consequences (glanz, rimer and lewis 2002) . in addition, studies have found that perceptions of the risk of personal and family infection are associated with the willingness to engage in preventive behaviors including vaccination (kraut, graff and mclean 2011; kumar et al. 2012 ). in recent years, an affective dimension (e.g., fear, apprehension, worry, anxiety) has been added to the model and has proven to be a strong predictor of health behavior. according to ahorsu et al. (2020) , one unique feature of viral pandemics is the fear that it can affect a large percentage of the population. fear is a negative emotion evident in extreme levels of emotive avoidance in relation to specific stimuli barr, et al., 2008) as such, the potential utility of perceived vulnerability in the current context should be explored. in addition, previous studies directed at understanding the experience and response to an infectious disease outbreak have indicated that self-confidence in the ability to implement social isolation and protective measures is an important component of social distance and protective behavior adoption (balicer et al. 2010; zhang, kong and chang 2015) . self-confidence refers to people's beliefs in their ability to manage a difficult task despite existing barriers to doing so (bandura 1997) . self-efficacy is the belief that one has the skills and can successfully complete the behavior of interest despite barriers to doing so (rosenstock, strecher and becker, 1988; farooq, jeske and isoaho, 2019) . assessment of self-efficacy are critical for compliance with avoidant behaviors in a pandemic (schwarzer and fuchs, 1995) . such beliefs about their capabilities influence their behavior. during the 2009 influenza and sars pandemics, studies identified self-confidence as a strong predictor of engaging in preventive behavior (bults et al. 2011; cheng and ng 2006) . more recently, self-confidence has been positively associated with intentions to wash hands and utilize the appropriate etiquette when coughing (kim and niederdeppe 2013; yoo, choi and park 2016) . the assessment of adopting recommended social distance and protective behaviors has been found to be associated with additional socio-demographic factors. gender is an important factor in health behavior (barr, et al., 2008) . this point has been underscored in various studies conducted during the sars epidemic (bish and michie, 2010) and a recent meta-analysis of the association of gender and protective behaviors during respiratory disease pandemics (moran and del valle, 2016) . these studies indicate that women are more likely to adopt protective measures than men. it is possible that gender traditional roles of caring for the family drive women to adopt at a higher rate protective measures than men. while explanation of this association still requires more research, the empirical findings are consistent (bish and michie, 2010; moran and del valle, 2016) . the association between income and the willingness to adopt preventive behaviors is unclear. some studies have reported a direct effect, meaning that those with higher income and wealth are more likely to adopt protective measures (linn, guralnik and patel, 2010) yet, more recent reviews have argued that the association is not direct but mediated by perceived risks. given that income is positively associated with health awareness and risk perceptions, it might have an effect on the willingness to take preventive behaviors (nguyen et al. 2011) . following these arguments in this study we control for age, gender and income. the data for this study were collected through an online survey (google forms). a questionnaire with 55 items was e-mailed to undergraduate, graduate and professional students of a large, private, not-for-profit university in the city of sao paulo, brazil. there were no incentives used, we only asked to answer if possible and specified that it would help the university's research group to understand behavior j o u r n a l p r e -p r o o f during the challenging times of covid-19 while also declaring the estimated time that it would take to fill the survey (around 10 minutes). according to ethics guidelines of the surveys respondent's university, it was not necessary irb approval because there were no intrusive questions, no incentives and respondents were invited to participate and could decline to participate at all or drop out of the study at any step of answering the questionnaire. we've removed 39 respondents that chose not to report their race or gender. a total of 7,554 questionnaires were completed and no missing values were found. in terms of socio-demographic variables, 28 percent were men and 72 percent were women. in terms of age distribution, 65 percent were between 18 and 30 years old, and 30 percent were between 31 and 50 years old. thus, at least 95 percent of our sample was not in the over-60 category, which is the group with the greatest risk of contracting covid-19. as for income, 56 percent earned a monthly salary of between r$1,009 and r$3,566 (around usd $183 to usd $646 using the exchange rate of $1 usd equals 5.50 brl). the dependent variable is the adoption of protective measures. we asked respondents to indicate on a likert scale from 1 to 5 how frequently they engage in 18 behaviors. examples of the items are "wash your hands with soap and water," "avoid touching your mouth and nose with your hands," "cough in your elbow," "maintain at least a meter of distance from other people," "avoid visiting friends and family members not living with you" and "put on a face mask when going outside" (î±=.89). our independent variable is confidence in social institutions. to measure this concept, we used several variables. confidence in the government was measured with an item that asked the respondents to indicate "how confident are you in the government's ability to deal with the coronavirus pandemic?" confidence in the j o u r n a l p r e -p r o o f we introduced socio-demographic variables as control variables. age was measured as a continuous variable. gender was measured as a dummy variable with women coded 1 and men coded 0. marital status was measured as a series of dummy variables with single being the omitted category, and married, divorced and widowed j o u r n a l p r e -p r o o f included in the analysis. in order to measure income, respondents were provided with six categories of income and asked to indicate the one closest to their level. in table 1 the correlations between the variables in the analysis are presented in table 2 . overall, the correlations were low and moderate, so multicollinearity does not appear to be of concern. as expected, preventive behaviors were positively associated with self-confidence, and confidence in the hospitals, health workers and the media. however, there was a negative association between confidence in the government and preventive behaviors (r=-.007). indeed, the lower the confidence in the government the greater the number of preventive behaviors individuals adopted. in addition, there was a negative relationship between confidence in the government and vulnerability (r=-.019). together, these findings are an indication that, in the case of brazil, having a great deal of confidence in the government might be dangerous for the residents, as it is associated with fewer perceptions of vulnerability and a low level of adoption of protective behaviors. as expected, perceived vulnerability was positively associated with the number of behaviors adopted (r=.026). in the next step we conducted an ordinary least squares (o.l.s.) multivariate analysis. we used the hierarchical regression analysis approach with three block models (jaccard and turrisi, 2003) . we used r statistics version 4.0.0 using the built-in linear model function for the regressions. we tested for multicollinearity by assessing the variance inflation factors (vif) of all the variables. the vifs, in all models, ranged from 1.0 to 1.6, which tells us that our models did not suffer from multicollinearity. for all the models listed in table 3 , we included the mean estimate and 95% confidence intervals for all regression coefficients, along with the associate p-value (because of our large sample, care must be taken to interpret significance and one should rely on confidence intervals to estimate effect sizes). the the older the respondents the greater the number of protective behaviors they adopted. as to gender, women adopted more protective behaviors than men 95% ci [3.00, 4.20]. we found no difference in the behavior of married people and singles (95% ci capture 0). however, those who were divorced 95% ci [-2.90, -0.17] and j o u r n a l p r e -p r o o f widowed 95% ci [-10 .00, -0.73] were likely to adopt fewer protective behaviors than singles. income was also related to the adoption of protective behaviors 95% ci [0.33, 0.86], with those who earned more being more likely to adopt more protective behaviors. in the second model we added our independent variables. even after controlling for the socio-demographic variables, the variables were statistically significant. self-confidence in the ability to engage in the protective behaviors was positively related to the adoption of such behavior 95% ci we utilized a sociological perspective to identify the factors involved in people's choice to adopt preventive measures in the wake of covid-19. using recreancy theory, we explored the relationship between confidence, perceived risk and social behavior in the presence of social risks (freudenburg, 1993) . confidence in social institutions is a central concept in the recreancy theory (khodyakov, 2007; freudenburg, 2001) . it reflects the public's belief that social institutions have the competency, knowledge and ability to manage a major public health crisis and the perception that the policies developed by these institutions are in the best interests of the population (shao and hao, 2020) . in the case of the covid-19 pandemic in brazil, the voice of the government and the voice of health institutions and the media were not consistent in the evaluation of the risk and the social policy and responses required (freitas, silva and cidade, 2020) . as the correlation matrix and the regression model revealed, confidence in the government was negatively related to preventive behaviors, indicating that the more confident people were in the national government that rejected social distance measures, the less likely they were to adopt protective measures. in contrast, confidence in hospitals and health workers and the media were positively associated with the adoption of such behaviors. the differences in the role of confidence in social institutions on the adoption of protective behaviors apparently reflects the discrepancies and inconsistencies in the messages from the government and the messages from the media and health system. another component of recreancy theory is perceived vulnerability (sapp and downing-matibag, 2009 ). the theory posits a correlation between confidence in social institutions, perceived vulnerability and adoption of protective behaviors. as expected, vulnerability was correlated with both measures. those who felt more vulnerable were more likely to adopt protective measures. in addition, we found a correlation between vulnerability and confidence in the government and hospitals and mass media. as expected, there was a negative correlation between confidence in the government and vulnerability. the greater the confidence in the government's messages that tended to downplay the seriousness of the virus, the less likely people were to regard the disease as a threat or see themselves as vulnerable to it. however, confidence in the media worked differently. the alarming messages and constant reporting increased the perceived vulnerability and the number of protective actions taken. vulnerability reduced the confidence in the hospitals but also increased the number of protective actions taken. self-confidence was positively associated with trust in social institutions and vulnerability. in turn, the correlation matrix and the regression analysis showed that self-confidence had a positive effect on the adoption of preventive measures. this is an important finding indicating that adopting preventive measures requires that people feel they have the ability to do so successfully (bish and michie, 2010) . a possible explanation, reported in a recent comparative study on the adoption of protective measures in china and israel, is that self-confidence helps to overcome social constraints in the implementation of social distance and protective behaviors (liu and mesch, 2020) . without such self-confidence, social policies may not be effective and not achieve the goal of reducing the contagion. our final question has to do with the mechanism through which vulnerability and risk, the central concepts in recreancy theory, work. the theory highlights both concepts as having main effects on protective behaviors but does not consider the interrelationship between them (freudenburg, 2001) . we found that the effect of social institutions was not consistent, as confidence in the government actually reduced the number of preventive behaviors adopted. therefore, we investigated the possibility that perceived vulnerability, measured as the emotional feeling of fear and the cognitive evaluation of risk, mediated the effect of confidence social institutions on the adoption of behaviors. our findings indicate that the effect of vulnerability on protective behaviors depends on self-confidence, confidence in the government and confidence in health workers. thus, the effect of confidence in social institutions on the adoption of protective behaviors is enhanced or muted based on variation in levels of perceived vulnerability. this finding is the innovation of our study. it identifies a mechanism that was previously not mentioned with regard to recreancy theory on the j o u r n a l p r e -p r o o f way the central constructs of the theory motivate the adoption of protective measures during a pandemic. our study has various limitations. first, while the study includes a large sample of respondents, it is based on a population of students at a large university in the state of sao paulo. thus, the sample is limited in its representativeness of the population of brazil and cannot be generalized to the total population. future studies should investigate the extent to which our findings may be generalized. second, we found that vulnerability is an important mediator of the effect of confidence in social institutions on protective behaviors. given the centrality of this measure, future studies should conduct a more in-depth investigation of the sources of perceived vulnerability. one possible source is exposure to the media, including specific channels such as television and social media. however, additional sources should be included to understand the cognitive process through which people evaluate their personal risk, which is a central component of the vulnerability measure. finally, our measure of confidence in the government did not distinguish between the federal, state and local government. confidence in these institutions might vary. many people may have more positive assessments of the local government with which they interact more often than the federal and state governments that seem more remote. despite these limitations, our study makes an important and innovative contribution to the understanding of the factors associated with the adoption of protective behaviors during a worldwide pandemic. our main contribution is in highlighting the mediating role of vulnerability in the effect of confidence in social institutions on the adoption of social distancing and protective behaviors. j o u r n a l p r e -p r o o f j o u r n a l p r e -p r o o f j o u r n a l p r e -p r o o f the health belief model the fear of covid-19 scale: development and initial validation how will country-based mitigation measures influence the course of the covid-19 epidemic covid-19 spread in the uk: the end of the beginning empirical assessment of government policies and flattening of the covid 19 curve social distancing measures to control the covid-19 pandemic: potential impacts and challenges in brazil characterizing hospital workers' willingness to report to duty in an influenza pandemic through threat and efficacy based assessment perceived self efficacy in the exercise of control over aids infection pandemic influenza in australia: using telephone surveys to measure perceptions of threat and willingness to comply ecological enlightenment: essays in the politics of the risk society social network-based distancing strategies to flatten the covid-19 curve in a post-lockdown world perceived risk, anxiety, and behavioural responses of the general public during the early phase of the influenza (h1n1) pandemic in the netherlands psychosocial factor predicting sars affected regions the covid-19 pandemic in italy: policy and technology impact on health and non-health outcomes. health policy and technology. cottle, simon strong social distancing measures in the united states reduced the covid-19 growth rate: study evaluates the impact of social distancing measures on the growth rate of confirmed covid-19 cases across the united states covid-19 in brazil: advantages of a socialized unified health system and preparation to contain cases risk perception of coronavirus disease 2019 (covid-19) in china during quarantine predicting students' security behavior using information-motivation-behavioral skills model impact of non-pharmaceutical interventions (npis) to reduce covid19 mortality and healthcare demand how brazil became the second-worst covid-hit country in the world herd immunity": a rough guide unhealthy cities. poverty, race, and place in america risk and recreancy: weber, the division of labor, and the rationality of risk perceptions risk, responsibility, and recreancy a covid-19 as a global disaster: challenge to risk governance and social vulnerability in brazil the novel coronavirus outbreak: amplification of public health consequences by media exposure trust in medical organizations predicts pandemic (h1n1) 2009 vaccination behavior and perceived efficacy of protection measures in the swiss public trust and the development of health care as a social institution health behaviour and health jesus importation and early local transmission of covid-19 in revista do instituto de medicina tropical de sã£o paulo early assessment of anxiety and behavioral response to novel swine-origin influenza exploring optimistic bias and the integrative model of behavioral prediction in the context of a campus influenza outbreak behavioral change in influenza vaccination; factors influencing increased uptake of the pandemic h1n1 versus seasonal influenza vaccine in health care personal the social ecological model as a framework for determinants of the 2009 h1n1 influenza vaccine uptake in the us disparities in influenza vaccine coverage in the united states risk perceptions related to sars and avian influenza: theoretical foundations of current empirical research a state of trust when even the best laid plans go wrong attention to the media and worry over becoming infected: the case of the swine flu (h1n1) a meta-analysis of the association between gender and protective behaviors in response to respiratory epidemics and pandemics acceptance of a pandemic influenza vaccine: a systematic review of surveys of the general public governing covid-19 without government in brazil: ignorance, neoliberal authoritarianism, and the collapse of public health leadership on the front lines of coronavirus: the italian response to covid-19 another decade, another coronavirus social learning theory and the health belief model the penguin dictionary of politics united but divided: policy responses and people's perceptions in the eu during the covid-19 outbreak consumer acceptance of food irradiation: a test of recreancy theorem changing risk behaviors and adopting health behaviors: the role of self-efficacy beliefs. self-efficacy in changing societies confidence in political leaders can slant risk perceptions of covid-19 ina highly polarized environment the perception of risk just institutions matter: the moral and political logic of the universal welfare state amplifying panic and facilitating prevention: multifaceted effects of traditional and social media use during the 2015 mers crisis in south korea using social and behavioural science to support covid-19 pandemic response mortality underreporting in brazil: analysis of data from government internet portals the effects of sns communication: how expressing and receiving information predict mers preventive behavioral intentions in south korea media use and health behavior in h1n1 flu crisis: the mediating role of perceived knowledge and fear .600 *** .400 *** .420 *** key: cord-221717-h1h2vd3r authors: scabini, leonardo f. s.; ribas, lucas c.; neiva, mariane b.; junior, altamir g. b.; farf'an, alex j. f.; bruno, odemir m. title: social interaction layers in complex networks for the dynamical epidemic modeling of covid-19 in brazil date: 2020-05-16 journal: nan doi: nan sha: doc_id: 221717 cord_uid: h1h2vd3r we are currently living in a state of uncertainty due to the pandemic caused by the sars-cov-2 virus. there are several factors involved in the epidemic spreading such as the individual characteristics of each city/country. the true shape of the epidemic dynamics is a large, complex system such as most of the social systems. in this context, complex networks are a great candidate to analyze these systems due to their ability to tackle structural and dynamical properties. therefore this study presents a new approach to model the covid-19 epidemic using a multi-layer complex network, where nodes represent people, edges are social contacts, and layers represent different social activities. the model improves the traditional sir and it is applied to study the brazilian epidemic by analyzing possible future actions and their consequences. the network is characterized using statistics of infection, death, and hospitalization time. to simulate isolation, social distancing, or precautionary measures we remove layers and/or reduce the intensity of social contacts. results show that even taking various optimistic assumptions, the current isolation levels in brazil still may lead to a critical scenario for the healthcare system and a considerable death toll (average of 149,000). if all activities return to normal, the epidemic growth may suffer a steep increase, and the demand for icu beds may surpass 3 times the country's capacity. this would surely lead to a catastrophic scenario, as our estimation reaches an average of 212,000 deaths even considering that all cases are effectively treated. the increase of isolation (up to a lockdown) shows to be the best option to keep the situation under the healthcare system capacity, aside from ensuring a faster decrease of new case occurrences (months of difference), and a significantly smaller death toll (average of 87,000). although we have experienced several pandemics throughout history, covid-19 is the first major pandemic in the modern era. the last critical global epidemic occurred in 1918 and became known as the spanish flu. but, in 1918, the reality was quite different. scientific and medical knowledge was much more limited, making it difficult to fight the disease. furthermore, the world was not globalized, the means of transport were not as agile as the current ones and the population was much smaller. the 21st century is marked by globalization and an intricate and intense social network, which connects in one way or another to everyone on the planet. the latter fact increases the danger that a local epidemic disease will rapidly evolve into a pandemic like what happened in wuhan, china, and now is all over the world. the form of propagation and contagion of the sars-cov-2 virus occurs by direct contact between individuals, through secretions, saliva, and especially by droplets expelled during breathing, speeching, coughing, or sneezing. the virus also spreads by indirect contact, when such secretions reach surfaces, food, and objects [41] . besides, infected people take a few days to manifest symptoms, which can be severe or as mild as a simple cold. there is even a large proportion of infected people who remain asymptomatic [37] . this makes it practically impossible to quickly identify the infected and apply effective measures to limit the spread of the disease. also, sars-cov-2 was discovered in december 2019, which makes it very recently in the face of the current epidemic. little is known about the covid-19 disease, which appears to be highly lethal, with no drugs to prevent or treat. the concern is greater since direct (individual -individual) and indirect (individual -objects -individual) social relations are the means of spreading the disease. thus, the social interaction structure is the key to create strategies and guide health organizations and governments to take appropriate actions to combat the disease. one of the main concerns is overloading the health system. the first case in brazil was confirmed on february 26, a 61-year-old man who traveled to the lombardy region in northern italy. now, in the middle of may, there are more than 200,000 cases and 14,000 deaths in all states of brazil [30] . the concern is even worse due to the country's social inequality, over 80% of the population relies solely on the public health system and this distribution is not uniform. according to [11] , there are only 9 hospital beds per 100,000 people in the north region while southeast accounts for 21 hospital beds. the treatment of severe cases requires the use of respirators/ventilation in intensive care units (icu), and if simultaneous infections occur there will be no beds to meet the demand and a possibly large number of victims. thus, it is urgent to develop models and analyses to try to predict the evolution of the virus. also, as noted in figure 1 , brazil is running towards being the next epicenter of the pandemic. it has already exceeded the number of cases in important countries such as germany, china, japan, italy, iran, south korea, and france (the rates consider the population size of each country and are on a logarithmic scale). [24] ). it is possible to notice that brazil is surpassing countries such as italy, south korea, japan, and china, and it is reaching the relative number of cases in the united kingdom and france. as of the date of this study, the united states is the epicenter of the pandemic. since covid-19 presents a unique and unprecedented situation, this work proposes a specific model for the current pandemic. based on the classic epidemic model sir, also extended to sid [35] , siasd [9] and siqr [14] , we propose a more realistic model to better represent the effects of the covid-19 disease by adding more infection states. the proposed approach also considers social structures and demographic data for complex network modeling. each individual is represented as a node and edges represent social interaction between them. the multi-layer structure is implemented by different edges representing specific social activities: home, work, transports, schools, religious activities, and random contacts. the probability of contagion is composed of a dynamic term, which depends on the circumstances of the social activity considered, and a global scaling factor β for controlling characteristics such as isolation, preventive measures, and social distancing. the proposed model can be used to analyze any society given sufficient demographic data, such as medium/big cities, countries, or regions. here we analyze in depth the brazilian data. the sir model is applied through the network using an agent model, and each iteration of the system is simulated using the 24-hour pattern, allowing us to understand the dynamics of the disease throughout the days. the results show the importance of social distancing recommendations to flatten the curve of infected people over time. this is currently maybe the only way to avoid a collapse of the health system in the country. the paper is divided as follows: section 2 presents important concepts about complex networks, the sir model and its applications. section 3 explains our proposed approach and sections 4 and 5 presents the results, discussion, and conclusions of the work. created from a mixture of graph theory, physics, and statistics, complex networks (cn) are capable to analyze not only the elements themselves but also their environment to find patterns and obtain information about the dynamics of a system. as most of the natural structures are composed of connected elements, graphs are suitable to analyze most of the real-world phenomena. over the past two decades researchers have been showing that many real networks do not present a random structure, and its emergent patterns can be used to understand and characterize a model [8, 39] . complex network analysis has then been applied to sociology, physics, nanotechnology, neuroscience, biology, among other areas [12, 13] . to start with a formal definition, a graph g is a set {v,e} where v is composed by n vertices (also known as nodes or elements) {v i , v n } and e is the set e(v i , v j ) of edges (or connections) among its elements. edges represents the relationships between two elements and its value can also represent the strength or weight of a connection if usually, applications with complex networks consist of two main steps: i) transform the real structure into a complex network, and ii) analyze the model and extract its features or understand its dynamics. one natural phenomenon that has a straight forward connection to a complex network in society. people are connected due to several aspects such as members of a family, religious groups, co-workers, members of the same school, or faculty, among other social relationships. therefore cns have been widely employed for social network analysis [38] . extended from social interactions, the epidemic spread has also been studied by researchers in the last decades. in this context, one of the best known and widely used epidemic models in infectious diseases is the susceptible-infectedrecovered (sir) model, which is composed of three categories of individuals [4, 7] • susceptible: the ones who are not infected but could change its status to a state to infected if in contact with a sick person combined with a probability β of contagion • infected: the ones that have the disease • recovered: usually after some time, a person recovers from the illness and it is not able to be infected again due to the immunity process (in this case, this is an assumption of the process). the recovery rate of infected people is aligned with a probability of γ also, the model can be described as where s, i and r represents the ratio of susceptible, infected and recovered people in the population, respectively. usually, the problem is solved with differential equations, however, agent-based techniques in networks can represent the nature of the spread of viral diseases in a more complex scenario. if a network is fully connected, meaning that e(v i , v j ) = {1, ∀ i,j 0 < i, j <= n }, equation 2 fits the structure perfectly. however, in the real world, not everyone is connected and people only contract the disease if in contact with an infected individual or object. this is why a complex network approximates the dynamics of real viruses and can help us to understand the disease behavior. there are various approaches to represent people and society as networks, named social network analysis. small world networks [32] can be used as a good approximation of the social connections. in 2000, moore [32] emphasized that the use of small-world networks, where the distance among two elements is usually small in comparison to the size of the population, showed a faster spread of the viral disease than classical diffusion methods. the approximation of real social phenomena was first explained by milgram [29] in [29] , the sociologist is the author of the well-known idea that there are up to six people separating any two individuals in the world, which reinforces the importance of analyzing the epidemic spread from a graph view. in [33] , the authors used small-world networks to simulate a sir model, however, they considered that every contact with an infected person resulted in contamination, which is not realistic. therefore, other researchers improved the model over the years, adding new constraints to approximate the simulation to real scenarios [15] . the sir model on networks works as follows: each node represents a person and, the elements are connected according to some criteria and the epidemic propagation happens through an agent-based approach. it starts from a random node, and for each time step nodes with the susceptible state can contract the disease from a linked infected node with a predefined probability. the same idea occurs with the recovered category. after a certain period, a node can recover or can be removed from the system (case of death) according to a certain probability. at the end of the evolution of a sir model applied to a network, the number of nodes in each sir category (susceptible, infected and recovered) can be calculated for each unit of time evaluated and then compare these data with real information, for example, the hospital capabilities of the health system. also, the probability of infection and recovery can be adjusted over time considering social distancing, hygiene, and health conditions. the proposed model extends the sir model to a more realistic scenario to achieve a better correlation to the covid-19 disease, since the model was created specifically for the disease, we named the model as complexvid-19. our strategy is based on a multi-layer network to represent the brazilian demography and its different characteristics of social relationships. each layer is composed of a set of groups representing how people interact in a given social context. in the network, a node represents a person and the edges are the social relationships between persons, and they are also the means through which the disease can be transmitted. the virus spreads from an infected node to neighboring nodes at each iteration step (1 step = 1 day), according to a given infection probability. first, we describe how the layers are built based on social data from brazil. to define the different social relations, the first information needed is the age distribution so that groups such as schools and work can be separated. we consider the brazilian age distribution in relation to the total population in 2019 [20] , details are given on table 1 . this distribution is used to define an age group for each node, which is then used to determine its social activities through the creation of edges on different layers. in this approach, each network-layer represents a kind of social relationship or activity that influences the transmission of the covid-19. in this way, it is possible to evaluate and understand what is the impact of each social activity in the epidemic propagation. basically, in this work, a network layer is represented by a set of edges connecting some nodes. the following social activities are considered, composing 6 different layers: • home: in this layer, all people that live in the same residence are connected. • work: connects people that work in the same environment/company. • transport: this layer represents people that eventually take the same vehicle at public transports. • school: represents the social contact of students that belong to the same school class. • religious activities: connects people of the same group of some religious activity. • random: this layer represents activities of smaller intensity, such as indirect contact (through objects/surfaces). the first layer represents home interactions and is composed of a set of groups with varying size which are fully connected internally. these groups have no external connections, i.e. the network starts with disconnected components representing each family. to create each group, we consider the brazilian family size distribution for 2010 [19] , the year with more detailed information on family sizes from 1 up to 14 members. we consider the probability of a family having sizes from 1 to 10, therefore the probability of a family having 10 persons is the sum of the higher sizes, the details of this distribution are given in table 1 . the first layer is then created following the family size distribution and ensuring that each family has at least 1 adult. figure 2 (a) shows the structure of such a layer built for a population of n = 100. a large fraction of the population in any country needs to work or practice some kind of economic activity, which also means interacting with other people. thus, work represents one of the most important factors of social relations, which is also very important in an epidemic scenario. to represent the work activity we propose a generic layer to connect people with ages from 18 to 59 years, i.e. 60% of the total population in the case of brazil. there is a wide variety of jobs and companies, therefore it is not trivial to create a connection rule that precisely reflects the real world. here, we consider an average scenario with random groups of sizes around [5, 30] , uniformly distributed, and internally connected (such as the "home" layer). an example of this layer is shown on figure 2 (b), using n = 100. although the nodes of a group are fully connected, the transmission of the virus depends directly on the edge weights, which we discuss in-depth on section 3.1.1. collective transports are essential in most cities, however, it is one of the most crowded environments and plays an important role in an epidemic scenario also due to the possibility of geographical spread, as vehicles are constantly moving around. the third layer we propose represents this kind of transports, such as public transports, and includes people that do not possess or use a personal vehicle. in brazil the number of people using public transport depends on the size of the city, with 64.98% in the capitals and 35.89% in other cities [23] , with an average use of around 1.2 hours a day 1 . here we consider the average of the population between the two cases (50%), randomly sampled, to participate in the "transports" layer. random groups are created with sizes between [10, 40] , uniformly sampled, and the nodes within each group are fully connected. this variation of sizes is considered to represent cases such as low and high commuting times, and also the differences between vehicle sizes. other factors such as agglomeration and contact intensity are discussed in section 3.1.1. this layer is illustrated on figure 2 (c). schools are another environment of great risk for epidemic propagation. the proposed layer considers the characteristics of schools from primary to high school and how children interact. we consider that all persons from 0 to 17 years (24% of the brazilian population) participate in this layer, and the size of the groups, which represents different school classes, varies uniformly between [16, 30] [21]. this layer is illustrated on figure 2 (d). brazil is a very religious country, in which by 2010 only around 16.2% of the population claimed not to belong to any religion [18] . 64.6% claimed to be catholic and 22.2% to be protestant, summing up to 86.8% of the total population. here we consider that nearly half of these people (40% of the total population) actively participate in religious activities (weekly). the distribution of religious temple sizes is defined as a pareto distribution in the interval [10, 100] . taking into account that wage distribution follows the pareto distribution approximately, we model real estate predominance according to their capacity. the assumption here is that building costs (for churches, offices, homes, etc.) have a linear relationship to their internal capacity, and thus any given capacity has a power-law relationship with the number of such buildings within a region. we consider a random layer to represent all kinds of contacts not related to the specific previous social layers. this includes small direct contacts (person-to-person) and indirect contacts (individual -objects -individual) that may happen throughout the week, such as random friend/neighbor meetings, shopping, and other activities that involve surface contacts. for that 5n new random edges are created, that can connect any node. on the one hand, this yields an average of 5 random connections to each node, which can randomly connect any other node. on the other hand, the impact of this layer on the epidemic is smaller than the others, as it represents rapid contacts in comparison to the other activities described, thus its infection probability is smaller. in the following section we discuss the details concerning this aspect, deriving from the edge weights of each layer. in figure 2 (f) an example of this layer is shown. the overall structure of social interactions in our model can be compared to the statistical analysis in [16] , however here we introduce a more detailed model of social contacts with specific layers and connection patterns to better fit the particularities of a given country or city. unlike the traditional sir model, which consists of a single β term to describe the probability of infection, here we propose a dynamic strategy to better represent the real world and the new covid-19 disease. the idea is to incorporate important characteristics in the context of epidemic propagation according to each layer. firstly, to a given layer a fixed probability term is calculated to represent its characteristic of social interaction. for this, we considered 3 local terms: the contact time per week, the average number of people close to each other (agglomeration level), and the total number of people involved in the respective activity. considering two nodes v x and v y , connected at group j of layer i, its edge weight is then defined by where t i represents the average weekly contact time on layer i, k i is the agglomeration level (average number of nearby people) and n ij represents the size of the group j in which the nodes participates on layer i. the first fraction represents the contact time normalized by the total time of the week (24 * 7 = 168), and the second fraction represents the proportion among the local people closest to the total number of people on that activity group. the first part of the infection probability equation is multiplied by a β term, which scales the original probability. the β term is then the only parameter to tune the infection rates for the entire network, and the other properties are specific for the studied society, based on its population characteristics and the nature of the activities (layers). table 2 shows these specific properties that we considered for the brazilian population, and how the infection probabilities are calculated for each layer. in the table, we have the following information: who or how many people are part of the activity represented by a layer (column "who", discussed in the previous section); contact time according to activity (column "time of contact"); the average number of people close to each other in each activity (column "nearest", represents the agglomeration level); the number of connections between people (column "group size"); the probability of infection (column "probability"). • susceptible: traditional case, it means that a person can be infected at any time. this is the initial state of every node. • infected -asymptomatic: people who do not show any symptoms (30% of the total cases of infection) and remain contagious for up to 18 days (they may recover after 8 days). this is the most dangerous case for the epidemic spreading because the person is not aware of its infection. • infected -mild: 55% of the cases, present mild and moderated symptoms with no need for hospitalization, remain contagious for up to 20 days, and may recover after 10 days of infection. • infected -severe: 10% of the cases, present strong symptoms, and need hospitalization, remain contagious for up to 25 days. has a death rate of 15% and may recover after 20 days. • infected -critical: present worst symptoms and remain contagious for up to 25 days, need icu and ventilation, have a death rate of 50% and may recover after 21 days. • recovered: people who went through one of the infection cases and overcame the disease, ceasing to contaminate and supposedly becoming immune. these nodes no longer interact with other nodes anymore and are therefore removed from the network. • dead: people who went through severe or critical cases and eventually died. these nodes are also removed from the network. estimates for the proportion of asymptomatic cases vary from 18% (95% confidence, [15.5, 20 .2%]) [31] to 34% (95% confidence, [8.3, 58 .3%]) [17] . considering the confidence intervals, here we roughly approximate it to an average of 30% of the total number of infected cases. however, it is very difficult to study asymptomatic cases due to several reasons, such as the lack of available tests and the difficulty in identifying potential cases, which would include every person who had contact with known symptomatic cases. some studies indicate that asymptomatic cases may remain contagious for up to 25 days, with an incubation period of 19 days [6] , but the viral load may be smaller at the end of the infection. here we take an optimistic approach considering that they may recover (become immune and cease to contaminate) uniformly after 8 days of infection, up to around 18 days. as for the recovered nodes, we are considering that people become immune or at least acquire a long-term resistance to the virus, up to a maximum of 300 days (limit of our simulations). however, this should be taken cautiously as these properties are not yet fully understood [26] . the infection grows through the contact (edges) between infected and susceptible nodes, and the probability of being infected is the edge weight. if infection occurs, then one of the 4 infection cases are chosen based on the probability described above (30%, 55%, 10% and 5%). this distribution plays an important role in the structure and dynamics of the network. the node structure of asymptomatic cases does not change during the simulation, except for the time it takes to cease contamination and recover. it means that as these persons are not aware of their contamination, they will remain acting normally on the network (according to the active layers and edge weights). their contagious time varies from 1 to 18 days after infection. concerning the other cases (mild, severe, and critical), we consider the incubation time of the virus, the recovery time, the contagion time, the death rates of each case, and the usual action taken by the infected person or health professionals at hospitals. various works [5, 27, 28] point out that the average incubation period of covid-19 is around 5 days, but some cases may take much less or more time. the official who report [40] states that the average incubation time is around 5 to 6 days, with cases up to 14 days. the results in [27] show that the average shape of the incubation time follows a log-normal distribution (weibull distribution) with an average of 6.4 days and a standard deviation of 2.3 days. in this context, we consider the day when an infected person begins to show symptoms by randomly sampling from this distribution (1000 repetitions), with cases varying from 2 to 14 days. for mild cases, the nodes are isolated at home, maintaining the connections of the first layer, and then only 20% of the cases are diagnosed. considering the ratio of diagnosed cases, patients who are asymptomatic or with mild symptoms of covid-19 may not seek health care, which leads to the underestimation of the burden of covid-19 [25] . moreover, our diagnosis rule is also based on the fact that ongoing tests in brazil are increasing more slowly than in most european countries and the usa (tests are being performed mostly on people that need hospitalization). if a given case is severe or critical, the patient goes to a hospital and is fully isolated, i.e. we remove all of its connections. this is a rather optimistic assumption, considering that these patients still may infect the hospital staff. concerning the time that patients usually stay at hospitalization/icu, the works [10, 44] points to an average of 14 days for all cases. for standard hospitalization, we considered a minimum of 6 days and a maximum of 16 days of stay, and for the icu/ventilation, a minimum of 7 and a maximum of 17 days of stay. the time of each case will depend on the day the symptoms start and the day of recovering/death. figure 3 illustrates all the infected states and mechanisms described here. this configuration results in an overall lethality of 4%. it is important to stress that here we consider a maximum of 25 days of infection time, which is the time frame based on most studies we have seen so far in the literature. we are still at the beginning of the pandemic and a better characterization of the long-term impact is very difficult. nonetheless, the available information allows to represent the most obvious features of the sars-cov-2 virus and to evaluate its main impacts on society. to simulate the reduction or increase of social distancing/quarantine, we remove/include some layers of the network, or change their edge weights. similarly to the approach on [16] to improve home contact when in quarantine, we increase the home layer edge weights by 20% for each removed layer. to balance that we considered a smaller number of hours of contact in the base calculation for the home layer (3 hours a day), also taking into consideration that this layer has full contact between people of the same family. when the home contacts are increased according to our approach of layer removal, the time/intensity of contacts may increase up to its double. for each experiment with the proposed model, we consider the average and standard deviation (error) of 100 random repetitions to extract statistics of infection, death, and hospitalization time. due to the random nature of these networks, it is possible that extreme cases occur within the repetitions, i.e. when the infection starts at a node that is not capable of further propagation, leading the epidemic to end at few iterations. considering the real data we know that this is not the case, at least not for brazil, therefore we manually remove these networks and they are not considered for the average/error calculations. it is important to notice, however, that this rarely happens, in all our experiments we noticed a maximum of 4 networks of this kind. due to time and hardware constraints, our simulation considers 100,000 nodes, and the results need to be scaled up by a factor of 57 to match the brazilian population statistics. this factor was empirically found by approximating the model results in the number of reported cases in brazil. it is important to stress that for better statistics it should be considered the largest possible number of nodes to represent a population, i.e. the ideal case would be n = total country/city population. however, the computational cost of the simulation grows directly proportional to the number of nodes and edges of the network, and considering the critical situation of the moment at hand, 100,000 nodes are our limit to promptly present results of the epidemic dynamics. in the experiments when varying the social distancing, the same network is considered in each iteration, i.e. comparisons of including/excluding layers are made in the same random network. we considered the epidemic began on february 26, which is the day the first confirmed case was officially reported. it is important to emphasize that we made various optimistic assumptions throughout the model construction and simulation, such as to consider that people are behaving with more caution by reducing direct contact, wearing masks, and doing proper home/hospital isolation when infected. it is also important to notice that we are not considering the number of available icu/regular hospitalization beds for the death count, i.e. all the critical and severe cases are effectively treated. it is not trivial to estimate the direct impact of these numbers on the epidemic, however, this is an essential factor that directly impacts the number of deaths. here we focus on the impacts of different actions on the overall epidemic picture, such as the increase and reduction of cases, deaths, and occupied beds in hospitals. the social network starts normally, with all its layers and the original infection probabilities. the infection starts at a node with the closest degree to the average network degree and propagates at iterations of 1 day (up to 300 days). we consider an optimistic scenario, in which people are aware of the virus since the beginning, thus the initial infection probability is β = 0.3. this represents a natural social distancing, a reduction of direct contacts that could cause infection (hugs, kisses, and handshakes), and also precautions when sneezing, coughing, etc. we empirically found that this initial value of β yields results with a higher correlation to the brazilian pandemic. a moderated quarantine is applied after 27 days, representing the isolation measures applied on march 24 by most brazilian states, such as são paulo [1]. to simulate this quarantine we remove the layers of religious activities and schools and reduce the contacts on transports and work down to 30% of its initial value, i.e. β = 0.09. the remaining activities on these layers represent services that could not be stopped, such as essential services, activities that are kept taking higher precautionary measures, and also those who disrespect the quarantine. we compare the output of the model in the first 83 days with real data available from the brazilian epidemic (up to may 18) [24, 34, 42, 43] . the model achieves a significant overall similarity within its standard deviation. the greatest difference in the number of diagnosed cases at the last 10 days may be related to the increase in the number of tests being performed in brazil, or yet, the constant decrease of isolation levels in the country (below 50% for most days of the past month) [22] . we considered here a fixed isolation level around what was observed in the first days after the government decrees in brazil, but data in ref. shows that these levels are constantly changing. therefore, the number of diagnosed cases and deaths for the remaining simulation may be greater than the reported on this paper (see the "keep isolation" scenario in the next section). concerning the daily death toll, the average number of the proposed model is greater than the official numbers. this is somehow expected, considering that the underdetection rates may be greater in contrast to the fewer number of tests being performed. to better understand this, we analyzed the number of death in brazil from january 1 to april 30, comparing cases between 2019 and 2020, the results are shown in figure 5 . it is possible to observe a clear increasing pattern after february 26, which is the day of the first officially confirmed case of covid-19 in brazil. this indicates that the real death toll for the disease may be significantly greater than the official numbers. [24] , and world health organization (who) [42] . the dotted lines represent the standard deviation, in the case of the real data the curve is the average over a 5-day window, and the solid lines the real raw data. the greatest average number of deaths produced by the proposed model may be related to underdetection (see figure 5 ). [2] . then the total death difference is compared to the covid-19 records of the who [42] and the brazilian government [2] data. the largest difference that appears right after the first confirmed case may indicate a significant underdetection of covid-19 cases. after the initial epidemic phase, we consider 4 possible actions that can be taken after 90 days (may 26): a) do nothing more, maintaining the current isolation levels; b) stop isolation, returning activities to normal (initial network layers and weights); c) return only work activities, restoring the initial probability of the layer; or d) increase isolation, stopping the remaining activities in the work and transports layers (home and random remains). firstly, we analyze the impacts on the number of daily new cases and deaths, results are shown in figure 6 . as previously mentioned, at the start of the covid-19 pandemic, brazil was performing a fewer number of tests by an order of magnitude, in comparison to other countries with similar epidemic numbers, therefore we considered as diagnosed only the severe and critical cases, which are pronounced subjects for testing, and 20% of the mild cases. the total infection ratio is discussed later. considering keeping the current isolation levels, the peak of daily new cases occurs around 100 days after the first case (june 5), with around 11,000 confirmed cases. after 202 days (september 15), the average daily cases is around 500, and it goes below 100 daily cases after around 237 days (october 19). the peak of daily new deaths occurs around 118 days (june 23), with an average of 1900 deaths, and goes below 100 new occurrences after around 210 days (september 24). it is important to stress that this is a hypothetical scenario where the isolation level remains the same from day 27 to 300, which is hardly true in the real world where it is constantly changing [22] . the total numbers after the last day (300) account for 946,830 (±10, 507) diagnosed cases and 149,438 (±3, 124) deaths. when we consider the return of all activities after 90 days, the number of cases and deaths grows significantly in an exponential fashion. the peak occurs at 108 days (june 13) with an average of 40,937 (± 11,010) new cases, and at 122 days (june 27) with an average of 6,484 (± 1,739) new deaths. although the peak of cases/deaths and the decrease of the numbers occur early, in this case, the final result is critically worse, with a total of 1,340,367 (± 18,513) diagnosed cases and 212,105 (± 4,359) deaths. here it is important to notice that we considered that all the activities return after 90 days and remain fully operational until the last day (300). moreover, we do not account for the overloading of hospitals, which directly impacts the final death count. therefore, the number of deaths may be considerably higher. another possible scenario is the return of only the work layer, keeping reduced transports and no schools and religious activities, however, the pattern is similar to returning all activities, considering the growth time, peak, and decay time. the final numbers in this case are 1,253,119 (± 26,009) diagnosed cases and 197,756 (± 5,693) deaths. if the isolation is strictly increased after 90 days (lockdown), the infection and death counts drop significantly in comparison to the other approaches. moreover, the recovering time is much faster, as daily new cases stop earlier than the other scenarios. the peak of daily new cases happens around day 93 (june 1), and of daily new deaths around day 106 (june 11). the total numbers of diagnosed cases and deaths after day 300 are, respectively, 552,855 (± 195,802) and 87,059 (± 30,871). considering the hospitalization time described in the scheme of figure 3 it is possible to estimate the number of occupied beds for regular hospitalization (severe cases) and icu/ventilation (critical cases). we also show the difference between the cumulative growth of diagnosed and undiagnosed cases and recovered cases. the same approach as the previous experiment is considered (except for "return work") with 3 possible actions after 90 days (may 26), results are shown in figure 7 . the overall pattern of results is similar to the previously observed for the number of diagnosed cases and deaths. it is possible to notice that the number of undiagnosed cases is much higher than the diagnosed cases. this reflects the number of asymptomatic cases and the lack of tests for mild cases. in the worst scenario, which means ending the isolation, the total infected number may go above 5 million cases. the recovered rate is directly proportional to the infected rate, as one needs to be infected to either die or become resistant to the disease. if the infected rate is high, so is the recovered rate, e.g. the scenarios of keeping or ending isolation, and a high recovered rate also helps in mitigating the epidemic propagation (natural immunization). however, increasing isolation decreases the propagation much faster than natural immunization, with a considerably smaller death toll. it is also possible to observe the differences at the start of effective recovering, i.e. when the recovered rate surpasses the infected rates, this is due to the early increase in isolation levels. the peak of hospitalization occupancy occurs around a week before the death peaks, in any scenario. in this case, icus are very important because critical patients are treated there, which represents the cases of higher death rates. within the "end isolation" setting, patients may occupy up to an average of 215,285 (± 48,682) regular beds and 109,520 (± 24,647) icu beds. these numbers are by far greater than entire brazil's capacity, as publicly-available and private icu beds sum up to 45,848 [3] . even considering the better scenario, i.e. the lower bound of the standard deviation, the number of occupied icu beds may reach around 86,000, which is also critical for brazil's capacity (almost 2 times it's capacity). in this setting of "end isolation", the healthcare system would surely collapse. when the isolation levels are kept, the numbers are significantly lower. however, the occupancy of 66,110 (± 16,759) regular beds and 33,470 (± 7,926) icu beds is still critical for the brazilian health system. considering the creation of new provisional icu units and good patient logistics, the situation may still remain under control during the peak of hospitalization occupancy. however, the results show that the hospital occupancy is prolonged considerably in this scenario, and they may stay functioning around their maximum capacity for up to a month (with an average of occupied icu beds above 30,000). when increasing the isolation the peak of occupied beds is smaller, with an average of 63,226 (± 20,682) regular beds and 31,816 (± 10,592) icu beds. moreover, the shape of the curve throughout the days is different and the final numbers are considerably smaller. the peak also occurs around a week earlier and then decreases much faster. this scenario would be preferable as it has much more chances of not overloading the brazilian healthcare system, relieving the hospital occupancy considerably faster and, therefore, contributing to the reduction of the number of deaths. this work presents a new approach for the modeling of the covid-19 epidemic dynamics based on multi-layer complex networks. each node represents a person, and edges are social interactions divided into 6 layers: home, work, transports, schools, religions, and random relations. each layer has its own characteristics based on how people usually interact in that activity. the propagation is performed using an agent-based technique, a modification of the sir model, where weights represent the infection probability that varies depending on the layers and the groups the node interacts, scaled by a β term that controls the chances of infection. the network structure is built based on demographic statistics of a given country, region, or city, and the propagation simulation is performed at time iterations, that represent days. here, we studied in depth the case of the brazilian epidemic considering its population properties and also specific events, such as when the first isolation measures were taken, and the impacts of future actions. brazil is a large and populated country with a wide variety of geographical location types, climates, and it also has a lengthy border with other countries to the west. it is a challenging setting for any epidemiological study. here we consider an average over all the country population, as we adjust the model output to match some statistics of the epidemic official reports. brazil is performing fewer tests in comparison to other countries at the same epidemic scale, however, it is known that testing for infection is always limited, either due to the low number of tests or to the velocity of infections which the testing procedure cannot keep up to. we then considered that only hospitalization cases and 20% of the mild cases are diagnosed. asymptomatic cases are not diagnosed and keep acting normally in the network, considering the active layers. regarding the isolation of infected nodes, we take some optimistic assumptions: mild cases (even those not diagnosed) are aware of its symptoms and isolate themselves at home. severe and critical cases are eventually hospitalized, and then fully isolated from the network (removal of all its edges). under the described scenario, the network starts with all its layers and β = 0.3, representing that people are aware of the virus since the beginning (even before isolation measures). after 27 days of the first confirmed case, the first isolation measures are taken where schools and religious activities are stopped and work and transports keep functioning at 30% of the initial scale (achieved further reducing the β term). different actions are then considered after 90 days of the first case: keep the current isolation levels, increase isolation, end isolation returning all activities to 100%, or returning only the work activities. the results show that keeping approximately the current isolation levels results in a prolonged propagation, as we are near the estimated peak (around june 5) with an average of 11,000 daily new cases and 1900 daily new deaths, and an average of 946,830 diagnosed cases (up to 3,6 million infected) and 149,438 deaths until the end of the year. in this scenario, hospitals may exceed its maximum capacity around june 11, but the efficient implementation of new icu beds and good logistic management of patients may still keep the situation under control. however, this is a very optimistic assumption, considering that our definition of "keep isolation" considers social isolation above 50% as registered at the beginning of the brazilian quarantine [22] . the social isolation levels in brazil are constantly decreasing even when we are still in a state of moderated quarantine, and it is possible to observe average isolation below 50% in most days of the past month (middle of april to middle of may 2020). moreover, the results show that this prolonged scenario may cause hospitals to keep functioning at maximum capacity for up to a month. when analyzing other possible scenarios the situation may be considerably different. relaxing isolation measures from now on causes an abrupt increase in the daily growth of cases and deaths, up to 5 times higher in comparison to the current isolation levels. even if only work activities return while schools, religion, and transport activities remain inactive/reduced, the impact is very similar to returning all the activities, with a possible number of above 1,34 million diagnosed cases (up to 5,2 million infected), and around 212,105 deaths until the end of the year. this is, again, a very optimistic assumption as we do not consider the hospital overflow to calculate the death toll. considering this aspect, icu beds may be fully occupied in early june, and around the middle of the month their demand may reach up to 134,000 beds, which is around 3 times higher than the entire country's capacity. the other alternative, which is the increase of isolation levels (lockdown), appears to be the only alternative to stop the healthcare system from entering a very critical situation. in this scenario, the growth in the number of daily cases and deaths would be mitigated, and faster. as we are near the peak of new cases at current isolation levels, estimated to be between the beginning and middle of june, increasing the isolation levels does not cause a significant impact on when the peak occurs or its magnitude. however, the disease spreading and the occurrences of new cases decrease much faster in this scenario in comparison to any other scenario studied here, with a difference of months. moreover, the final numbers are considerably smaller, with an average of 552,855 diagnosed cases (up to 2.1 million infected) 87,059 deaths until the end of the year. although the proposed method includes various demographic information for the network construction, and an improved sir approach to covid-19, it still does not cover all factors that impact the epidemic propagation. as future works, one may consider more information such as the correlation between the age distribution within the social organization and the clinical spectrum of the 4 infection types (e.g. severe and critical cases are mostly composed of risk groups). another possible improvement consists of increasing n (number of nodes of the networks), e.g. using a value near the real population of the studied society, which we avoided here due to hardware and time constraints (graph processing is costly). another important point regarding the obtained results is related to the "keep isolation" scenario, which may be underestimated as we take various optimistic assumptions and also consider a fixed isolation level based on previously observed data, while most recent data shows that these levels are decreasing [22] . therefore, during the network evolution, a possible improvement is the use of dynamic isolation levels to better represent reality. it is also possible to consider various scenarios for future actions, such as 2 or more measures of increasing/reducing isolation. this may allow the discovering of new epidemic waves if social activities return too soon after the isolation period, such as what happened in 1918 with the spanish flu. portal da transparência -painel covid registral amib. brazilian intensive care medicine association: updated data on icu beds in brazil, 2020, visited on 2020-05-08 infectious diseases of humans: dynamics and control incubation period of 2019 novel coronavirus (2019-ncov) infections among travellers from wuhan, china presumed asymptomatic carrier transmission of covid-19 the mathematical theory of infectious diseases and its applications emergence of scaling in random networks modeling and forecasting the covid-19 pandemic in brazil covid-19 in critically ill patients in the seattle region-case series demand for hospitalization services for covid-19 patients in brazil analyzing and modeling real-world phenomena with complex networks: a survey of applications complex networks: the key to systems biology data analysis and modeling of the evolution of covid-19 in brazil epidemic spreading with awareness and different timescales in multiplex networks impact of non-pharmaceutical interventions (npis) to reduce covid19 mortality and healthcare demand clinical features of patients infected with 2019 novel coronavirus in wuhan, china tabela 137 -população residente, por religião tabela 185 -domicílios particulares permanentes por situação e número de moradores ibge. pesquisa nacional por amostra de domicílios contínua trimestral: tabela 5918 -população, por grupos de idade instituto nacional de estudos e pesquisas educacionais anísio teixeira: dados do censo escolar: ensino médio brasileiro tem média de 30 alunos por sala instituto de pesquisa econômica aplicada: sistema de indicadores de percepção social (sips) coronavirus resource center asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (sarscov-2): facts and myths positive rt-pcr test results in patients recovered from covid-19 the incubation period of coronavirus disease 2019 (covid-19) from publicly reported confirmed cases: estimation and application incubation period and other epidemiological characteristics of 2019 novel coronavirus infections with right truncation: a statistical analysis of publicly available case data the small world problem portal do covid-19 estimating the asymptomatic proportion of coronavirus disease 2019 (covid-19) cases on board the diamond princess cruise ship, yokohama, japan epidemics and percolation in small-world networks scaling and percolation in the small-world network model covid-19 coronavirus data model studies on the covid-19 pandemic in sweden the epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (covid-19)-china clinical characteristics of asymptomatic and symptomatic patients with mild covid-19 collective dynamics of 'small-world'networks world health organization -coronavirus disease 2019 (covid-19): situation report, 73 world health organization -modes of transmission of virus causing covid-19: implications for ipc precaution recommendations world health organization coronavirus disease (covid-19) dashboard clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study key: cord-356041-tc2cumv2 authors: cotrin, paula; moura, wilana; gambardela-tkacz, caroline martins; pelloso, fernando castilho; dos santos, lander; carvalho, maria dalva de barros; pelloso, sandra marisa; freitas, karina maria salvatore title: healthcare workers in brazil during the covid-19 pandemic: a cross-sectional online survey date: 2020-10-09 journal: inquiry doi: 10.1177/0046958020963711 sha: doc_id: 356041 cord_uid: tc2cumv2 brazil is in a critical situation due to the covid-19 pandemic. healthcare workers that are in the front line face challenges with a shortage of personal protective equipment, high risk of contamination, low adherence to the social distancing measures by the population, low coronavirus testing with underestimation of cases, and also financial concerns due to the economic crisis in a developing country. this study compared the impact of covid-19 pandemic among three categories of healthcare workers in brazil: physicians, nurses, and dentists, about workload, income, protection, training, feelings, behavior, and level of concern and anxiety. the sample was randomly selected and a google forms questionnaire was sent by whatsapp messenger. the survey comprised questions about jobs, income, workload, ppe, training for covid-19 patient care, behavior and feelings during the pandemic. the number of jobs reduced for all healthcare workers in brazil during the pandemic, but significantly more for dentists. the workload and income reduced to all healthcare workers. most healthcare workers did not receive proper training for treating covid-19 infected patients. physicians and nurses were feeling more tired than usual. most of the healthcare workers in all groups reported difficulties in sleeping during the pandemic. the healthcare workers reported a significant impact of covid-19 pandemic in their income, workload and anxiety, with differences among physicians, nurses and dentists. coronavirus disease 2019 (covid19) is an infectious disease caused by the novel coronavirus (sars-cov2). the world health organization (who) characterized covid-19 as a pandemic due to the rapid increase in the number of cases. to date, on july 24, 2020, there are more than 15 million confirmed cases of covid-19 worldwide, including 619,150 deaths. brazil has a current critical situation with the second-highest number of cases and deaths in the world. 1 963711i nqxxx10.1177/0046958020963711inquiry: the journal of health care organization, provision, and financingcotrin et al. inquiry unfortunately, an effective vaccine or medicine is not available to treat covid-19, and the most efficient strategies for controlling the covid-19 pandemic are preventive measures and social distancing. however, these interventions make this pandemic a problem more significant than a health crisis with an impact meaningful in societies, politics, and economies as a whole. 2, 3 in this context, the covid-19 pandemic causes concerns to the entire population, especially the health care professionals that are essential and continued to work and maintained patient care, despite the social distance and lockdown adopted in many countries. many of the healthcare workers are in the front line, in close contact with covid-19 infected patients, at high risk of infection and of transmitting the disease to their families and coworkers. 4 in brazil, there is lack of a homogeneous, transparent, and comprehensive surveillance system for covid-19 cases among brazilian health care workers during the covid-19 pandemic. 5 the coronavirus pandemic represents one of the greatest health challenges worldwide in this century, and this has a more devastating effect in third world countries, like brazil. an increase in the workload of healthcare workers during the covid-19 pandemic was reported in other countries, 6, 7 but the financial impact to these professionals were not yet fully reported, especially in brazil, that is facing an economic crisis that appears to be only in its beginning. to prevent infection and transmission of covid-19 by healthcare workers, the who and other national and international public health authorities recommended the use of appropriate personal protective equipment (ppe). however, a shortage of ppe is being observed as a result of the high demand considering the increasing number of cases. 3 in brazil, since the beginning of the pandemic, there is a great concern with the lack of ppe, low adherence to the social distancing measures suggested, and low coronavirus testing, indicating an underestimation of the number of cases in the country. 5, 8 another critical aspect regarding the protection of healthcare workers is the training to deal with covid-19 disease. a study performed with healthcare workers working in the national health service (nhs) across the united kingdom showed that approximately 50% of them did not receive proper training. 4 in addition to the risk of contamination, healthcare workers have suffered high-stress rates. many studies observed high rates of anxiety, stress symptoms, mental disorders, and post-traumatic stress among the healthcare workers during the pandemic. [9] [10] [11] [12] [13] [14] [15] primary care services are slightly superior as compared to traditional health care. in the brazilian health system, the first contact of patients occurs with professionals of the primary care service such as physicians, nurses and dentists. 16 however, with the covid-19 pandemic, there were changes in workload, jobs and general life of these professionals. this way, this study aimed to compare the impact of covid-19 pandemic in the healthcare workers: physicians, nurses, and dentists, regarding workload, income, ppe, training, behavior, feelings, and level of anxiety. this study was approved by the ethics research committee of ingá university center uningá, under number 31054320.6.0000.5220 and all participants agreed to participate in the survey. sample size calculation was performed with a confidence interval of 95% and margin of error of 5%, considering the application of a survey/questionnaire, with the number of physicians (496 422), 17 nurses (2 321 509), 18 and dentists (338 790), 19 in brazil, resulted in the need for at least 385 answers. the sample was randomly selected among the three categories of healthcare workers in brazil. a google forms (google inc, mountain view, ca, usa) questionnaire was elaborated and sent by e-mail and whatsapp messenger (whatsapp inc, mountain view, ca, usa) to 700 healthcare workers. inclusion criteria were: healthcare workers (physicians, nurses or dentists), above 22 years of age, working in the front line of the pandemic in private and public hospitals, healthcare units and private clinics, but not necessarily with direct contact with covid-19 infected patients. healthcare students were excluded from the sample. in the introduction of the questionnaire, the informed consent approved by the human research ethics committee was described, and the subjects were informed about the objectives. the participant's anonymity was ensured. the survey comprised questions about personal information, jobs, income, workload before, and during the pandemic. personal protective equipment (ppe) and training for covid-19 patient care and behavior during the pandemic were also assessed in the questionnaire. a structured questionnaire was developed and tested on a pilot population before its administration in this study. the pilot study was undertaken with 30 healthcare workers previously and randomly selected to clarity the questions and the language used. some words were rewritten with synonyms so that all participants were more likely to understand. the pilot study participants were not included in the main study. the levels of concern, anxiety, anger, and impact of the pandemic were evaluated with a numerical rating scale from 0 to 10. 20 to evaluate the intrarater agreement, one of the questions with yes/no responses was duplicated in the questionnaire. the answers to this duplicate question were compared using kappa statistics. the result showed a coefficient of 0.96, indicating an excellent agreement. 21 the percentage of distribution among the groups about sex, age, years of experience, income and workload information, knowledge about personal protective equipment (ppe), training to treat covid-19 suspected or infected patients, and behavior during the pandemic were assessed with chi-square tests. the one-way anova and tukey tests were used for the intergroup comparison of the levels of anxiety and confidence about work, anger, concerns with family, and the influence of pandemic in the relationship with patients and the work team. statistical analyzes were performed by statistica software (statistica for windows, version 10.0, statsoft, tulsa, okla, usa), and the results were considered significant at p < .05. the response rate was 76.6% since a total of 536 healthcare workers answered the survey: 179 physicians (117 female; 62 males), 170 nurses (151 female; 19 male), and 187 dentists (125 female; 62 male). most healthcare workers were between 31 and 40 years old, and physicians were younger than dentists and nurses. females were the majority in all groups, but more significant in the nurses' group. physicians' respondents had fewer years of experience in the profession than nurses and dentists (figure 1 ; demographics). physicians and dentists had more jobs than nurses before the pandemic. with the pandemic, the number of jobs reduced in all groups, but significantly more in the dentists' group. workload before the pandemic was higher for physicians, followed by dentists, and then the nurses, that presented a significantly lesser workload. the majority of physicians and dentists reported a reduction in workload during the pandemic. the monthly income was higher for physicians, followed by dentists and lesser for nurses. the majority of physicians and dentists reported a change in the monthly income with the pandemic. the income was reduced significantly in all professional groups and maintained the same pattern of difference between the groups ( figure 2 ). almost all healthcare workers knew the who recommendations about the use of ppe. more nurses reported to have only partially the ppe, and more dentists have ppe in their work environment. more physicians and dentists reported that their work has ppe following the who recommendations than nurses, and approximately one-third of the healthcare workers reported that available ppe followed who recommendations. about half of the physicians and nurses were working directly with covid-19 infected patients, but the minority of dentists were. most healthcare workers did not receive training for treating patients suspected and infected from coronavirus ( figure 3 ). nurses were respecting the quarantine more than physicians and dentists. most of the healthcare workers believed that their positioning and behavior influence people around them, but physicians and nurses believed more than dentists. more dentists and nurses thought about giving up their jobs or professions after the beginning of the pandemic than physicians. in all groups, approximately 90% of the respondents reported being afraid of being infected by coronavirus in the clinical or hospital environment, and more than 95% of them changed habits fearing to contaminate their family members. the minority were pressured by family members to quit their jobs. more physicians and nurses were feeling more tired than usual than dentists. most of the healthcare workers in all groups reported difficulties in sleeping during the pandemic (figure 4) . dentists felt less prepared and confident to care for covid-19 patients than physicians, and nurses and dentists were more anxious and stressed with the pandemic. nurses believed that the pandemic will have a more positive impact on their profession and that the experience during the pandemic will have a more significant influence in their professional future than physicians and dentists. the level of concern about infecting family members was high (above 8 of 10) and similar between the three groups. physicians, nurses, and dentists were feeling comfortable similarly in providing patient care during the pandemic. nurses were feeling angrier than physicians and dentists. dentists reported being more anxious when providing patient care during the covid-19 pandemic than physicians. dentists answered that the relationship with the patient was more influenced by the pandemic than physicians and nurses, and the relationship of dentists with their work team was more influenced by the pandemic than physicians (table 1 ). this survey gives a broad outlook of the brazilian healthcare workers' views about the covid-19 pandemic. at first, it is necessary to bring the brazilian context in facing of the pandemic, mainly because the projections about the behavior of the pandemic and people related to it depend not only on scientific knowledge but mainly on quality and reliable data regarding the new disease, 5,22 and currently it is not possible in brazil. there is no clear leadership. 23, 24 since may 15, 2020, brazil does not have a health minister, and the governors and the president of the republic do not follow the same guidelines regarding the implementation of quarantine and medications. effective quarantines and lockdown measures were not even implemented in brazil. while the world scientific community says that only strict social isolation measures can slow the spread of the virus 25, 26 and that there is still no effective pharmacological treatment for covid-19, 27 the brazilian denialist actual president 24, 28 insists on reopening of business offices, schools and churches, he also is against the use of face masks. he makes open advertisements about a medicine whose studies have already been canceled by who because the medicine is not effective against coronavirus. 27 so, in brazil, there have been no federal guidelines for primary health care services in response to covid-19. 28 amid this situation, the healthcare workers do not know whether to follow the who recommendations or the president's denialist recommendations. the national response is, in practice, being guided by developments at the local level, without any semblance of central coordination. 28 healthcare in brazil is the responsibility of the municipalities, using the health unic system (called sus in brazil), including pandemic preparedness. it means that matters such as the provision of ppe, rules on social distancing, and testing arrangements vary. 24 starting from this specific information, it is then possible to begin to affirm that the covid-19 pandemic has burdened unprecedented psychological stress on people around the world, especially the medical workforce. 29 emotional and behavioral reactions that healthcare workers may experience during this crisis (e.g., difficulty sleeping, anger) are also being shared by the entire community. 30 healthcare providers are vital resources for every country, mainly in disruptive periods like this that we are facing. the intensive work drained healthcare providers physically and emotionally, 6 and the entire population trusts in the work of these professionals and hopes that they can carry out their tasks safely and correctly. therefore, it is essential to know the impact that the pandemic has had on health professions to promote strategies to counteract stressors and challenges during this outbreak. studies like this are necessary because mobilization now will allow public health to apply the learnings gained to any future periods of increased infection and lockdown, which will be particularly crucial for healthcare workers and vulnerable groups, and to future pandemics. 31 reporting information like this is essential to plan future prevention strategies. 10 the questionnaire was created using google forms and was sent via a link in a messaging app, e-mail and social media, and is in accordance with iqbal et al. 4 consolo et al 32 also used google forms to create their survey, but they sent it via an anonymous e-mail. in this study, a messaging app was chosen because they are practical and can be accessed quickly by cell phone, which facilitates the healthcare workers' response. most health care workers were in the 31 to 40 years age range (figure 1 ). lai et al 33 found similar results; however, the respondents of chew et al 9 were younger (age range: 25-35 years). this age difference, although not significant, may have been due to the methodology that the surveys were conducted. chew et al 9 survey was conducted directly at the healthcare workers' workplace, while this present study sends on-line questionnaires via messaging app. the greatest part of the respondents were females, and also the females were the majority in all health profession groups, but even so, greater in the nurses' group ( figure 1 ) other authors found similar results. 9,33 also, cross-sectional studies show minimal male participants in this type of study. 32, 34 besides that, women are more willing to participate in researches, 35 and the majority of nursing professionals in brazil are females. 36 the workload was reduced for physicians and dentists during the pandemic (figure 2 ). this reduction was observed because quarantines were recommended in several cities in brazil, and private practices, both for physicians and dentists, were closed for elective procedures. this result also justifies why the dentists and physicians had more jobs than nurses before the pandemic. most respondent nurses work in public health, with a predetermined workload, which has not been changed due to the pandemic. besides that, the income was significantly reduced in all professional groups (figure 2 ). it is known that a pandemic often brings economic recession, and this is what happened during the first quarter of 2020. 37, 38 this result is in agreement with a study about dental practitioners, 32 conducted in italy in the early stages of the pandemic, where all respondents reported practice closure or substantial activity reduction with serious concerns regarding their professional future and economic crisis. previous crises have shown how an economic crash has direct consequences for public 39 and this is no different for healthcare workers. with the increasing cases in brazil, it was expected that job opportunities would also increase, but this was not observed in this study, no new hires were made, which leads to the conclusion that the concern about the future financial impact is great among health professionals. however, this survey was conducted in an earlier stage of the pandemic, and now, in the peak, this scenario may have changed. it can be speculated that physicians and dentists have more ppe following who recommendations than nurses because as most of them work in their private practice, they bought the necessary ppe themselves, while the majority of the nurses work in public health, where ppe is sometimes not adequate (figure 3 ). ppe has gained even more importance in recent times because with the increased demand for use, ppe has become more expensive and scarcer. healthcare workers reported that there was limited access to essential ppe and support from healthcare authorities during the covid-19 pandemic from latin america to europe. 3, 4 some physicians related reusing face masks that are meant to be disposable because their hospitals may run out in the next few weeks. 30 consolo et al 32 related that 77% of the dentists in their study increased the use of ppe during the covid-19 pandemic. in addition to the professionals' inherent concern with ppe, in brazil there is also a concern about the shortage of supplies needed to treat the more severe patients, scarce availability of diagnostic tests and constant tension regarding the collapse of the icu beds available is also observed. 5 to date and exemplify, as of july 22, drugs used to keep icu patients sedated will end in four days on paraná state, in the south region of brazil. 40 about half of the physicians and nurses were working directly with covid-19 infected patients, but the minority of dentists were (figure 3) . a survey conducted in the united kingdom in the first two weeks of april showed similar results, where 95.26% of the healthcare workers had direct patient contact in daily activity. 4 dentists had less contact with infected patients because as already seen, their elective appointments were suspended due to the quarantine. 41, 42 in this scenario, it would be expected that healthcare workers have adequate training to care for patients infected with covid-19, but most healthcare workers did not receive this training. in a study conducted in the uk, half of the healthcare workers also reported that they did not have adequate training. as already stated here, this is an unprecedented event, so many countries, even the richest, are having difficulties in establishing training protocols for healthcare workers. besides that, dentists reported being more anxious when providing patient care during the covid-19 pandemic than physicians ( figure 3 and table 1 ). it is reasonable that dentists feel more anxious to assist patients during the pandemic, as it is known that the contamination rate of this disease is very high in aerosols and droplets, 43, 44 which makes the dental community a relatively high-risk population. however, it is essential to highlight that in the early stages of the pandemic, the brazilian ministry of health launched a national program called "brazil counts on me". 45 this program focused on training and registering healthcare workers to face the coronavirus pandemic. it seems that many professionals did not do this training offered by the government. moreover, a recent survey 29 showed that as compared to the non-clinical staff, front line medical staff with close contact with infected patients showed higher scores of fear, anxiety and depression. this implies that effective strategies toward to improving mental health should be provided to these individuals. 29 healthcare workers often feel fully responsible for the well-being of their patients. they usually face the challenges of work as their duty. 6 this has become more evident in recent times and could reflect in the way that they influence people around them, like respecting the quarantine, as an example. in this study, the majority of the healthcare workers believed that their positioning and behavior influence people around them, and physicians and nurses believed more than dentists (figure 4 ). one can say that physicians and nurses believed they have a more considerable influence on society than dentists due to the nature of their work. people, in general, tend to view physicians and nurses as essential professionals, and they tend to observe them as an example, even outside the work environment. so, it is natural for them to believe that their behavior can influence (in a positive way) the people around them. in all groups, approximately 90% of the respondents reported being afraid of contamination by the coronavirus in the clinical or hospital environment (figure 4) , agreeing with previous reports. 4, 32 this was probably the cause of more dentists and nurses thought about giving up their jobs or professions during the pandemic, although the minority of healthcare workers reported pressure from family members to quit their jobs ( figure 4 ). as already discussed above, several factors must be related to the insufficient training to care for infected patients, lack of adequate ppe, and decreased income. another point that must be taken into account is the amount of healthcare workers deaths by the coronavirus, which is alarmingly high in brazil. in may 2020, which was the early stage of the pandemic in brazil, brazil already surpassed the usa in deaths of nursing professionals by covid-19 and had more deaths than italy and spain combined. 18 most of the healthcare workers in all groups reported difficulties in sleeping during the pandemic (figure 4) . previous pandemic experiences showed that these reactions reflect a sense of fearful waiting, or even terror, about what the future may hold for all humankind while an unfamiliar and uncomfortable quiet fills the halls. 46 this is expected because the own nature of the pandemic and the unique characteristics and unpredictable evolution of the covid-19 disease, like a uniquely high risk of asymptomatic transmission and significant knowledge gaps about the viral pathophysiology 47, 48 can also lead to loss of sleep. recent studies showed that a significant part of the healthcare workers presented symptoms of insomnia. 9,33,34 all these features generate many uncertainties in healthcare workers, but, for the brazilian ones, the challenge is even greater, and the scenario is even scarier. additionally to the already established insufficient scientific knowledge about the new virus and its high speed of dissemination, 49, 50 little is known about the transmission characteristics of the covid-19 in a context of great social and demographic inequality. here in brazil, people are living in precarious housing and sanitary conditions, without constant access to water, in an agglomeration and with a high prevalence of chronic diseases. 22 nurses and dentists were more anxious and stressed with the pandemic, and nurses were feeling angrier than the other healthcare workers evaluated in this survey (table 1) . a recent systematic review showed that anxiety was the most prevalent mental health symptom during the pandemic. 12 studies on the mental health of the healthcare workers during the covid-19 pandemic showed that there are occupational differences regarding affective symptoms among healthcare workers, and nurses showed the highest levels. 34 besides that, nurses may face a higher risk of exposure to covid-19 patients as they spend more time in the front line, providing direct care of patients. 6 dentists, physicians, and nurses had a similar level of concern about infecting family members (table 1 ). it was observed that more physicians and nurses were feeling more tired than usual than dentists. this was expected, because, in addition to all the concerns inherent to the actual moment, these two categories of healthcare workers are dealing directly with infected patients, and there are also other contributing factors related to this: excessive workload and work hours, work-life imbalance, inadequate support, insufficient rewards, interpersonal communication, and sleep privation). 13 although many of the health care workers accept the increased risk of infection as part of their chosen profession, some may have concerns about family transmission or feel pressure to comply because of fear of losing their job, desire to be part of the team, and altruistic goals of caring for patients in need. 30 disruptive periods like this generate uncertainty and fear of the unknown, especially in the professional field. when asked how the covid-19 pandemic could influence the future of their professions, nurses were more optimistic than physicians and dentists. they believed that the pandemic would have a more positive impact on their profession. consolo et al 32 showed that ¾ of the respondent dentists reported that there had been an extremely negative impact on their practice. dentists believed that the relationship with the patient and their staff were more influenced by the pandemic than physicians and nurses (table 1) . this is understandable, as dentists usually have a very close relationship with their patients and staff. since the dental team is considered to be at high risk for covid-19 infection, dental offices had to prepare for providing care, improving communication with their patients, changing the routine of their dental offices, and improving the ppe of their employees and patients. in the long term, patients will notice these changes and will value professionals who care about them. on the other hand, according to consolo et al 32 there is a concern regarding the inability to prevent the end of the pandemic, followed by the impaired economy that might affect future patient turnover and the capability to pay for the dental practice expenses, which include buying further devices and to adequate to new clinical protocols to counteract the spreading of sars-cov-2. the number of jobs reduced to all healthcare workers during the pandemic, but this reduction was more significant for dentists. also, the workload and income reduced to all healthcare workers. almost all healthcare workers were aware of the who recommendations about the use of ppe. nurses related that their work has ppe partially following the who recommendations. most healthcare workers did not receive training for treating patients suspected and infected from coronavirus. physicians and nurses were feeling more tired than usual than dentists. most of the healthcare workers in all groups reported difficulties in sleeping during the pandemic. dentists reported being more anxious when providing patient care during the covid-19 pandemic than physicians. the author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article. the author(s) received no financial support for the research, authorship, and/or publication of this article. karina maria salvatore freitas https://orcid.org/0000-0001 -9145-6334 world health organization. coronavirus disease 2019 (covid-19) epidemiology of covid-19 in brazil: using a mathematical model to estimate the outbreak peak and temporal evolution personal safety during the covid-19 pandemic: realities and perspectives of healthcare workers in latin america covid-19: results of a national survey of united kingdom healthcare workers' perceptions of current management strategy -a cross-sectional questionnaire study covid-19 among health workers in brazil: the silent wave the prevalence and influencing factors in anxiety in medical workers fighting covid-19 in china: a cross-sectional survey impact of covid-19 outbreak on healthcare workers in italy: results from a national e-survey paho director calls for "extreme caution" when transitioning to more flexible social distancing measures a multinational, multicentre study on the psychological outcomes and associated physical symptoms amongst healthcare workers during covid-19 outbreak pandemic fear" and covid-19: mental health burden and strategies covid-19 and mental health: a review of the existing literature how essential is to focus on physician's health and burnout in coronavirus (covid-19) pandemic? cureus mental health and psychosocial problems of medical health workers during the covid-19 epidemic in china prevalence and influencing factors of anxiety and depression symptoms in the first-line medical staff fighting against covid-19 in gansu sus: supply, access to and use of health services over the last 30 years federal council of dentistry. general number of specialist dental surgeons visual analog scale versus numeric pain scale: what is the difference? the measurement of observer agreement for categorical data what is urgent and necessary to inform policies to deal with the covid-19 pandemic in brazil? covid-19 and orthodontics in brazil: what should we do? covid-19 in latin america impacts and effectiveness of quarantine in the outbreak of covid-19: a comparison among pandemics report 9: impact of non-pharmaceutical interventions (npis) to reduce covid19 mortality and healthcare demand a systematic review on the efficacy and safety of chloroquine for the treatment of covid-19 community health workers reveal covid-19 disaster in brazil psychological status of medical workforce during the covid-19 pandemic: a cross-sectional study healing the healer: protecting emergency health care workers' mental health during covid-19 multidisciplinary research priorities for the covid-19 pandemic: a call for action for mental health science epidemiological aspects and psychological reactions to covid-19 of dental practitioners in the northern italy districts of modena and reggio emilia factors associated with mental health outcomes among health care workers exposed to coronavirus disease 2019 prevalence of depression, anxiety, and insomnia among healthcare workers during the covid-19 pandemic: a systematic review and meta-analysis a nationwide survey of psychological distress among chinese people in the covid-19 epidemic: implications and policy recommendations general characteristics of nursing: the socio-demographic profile covid-19: implications for business covid-19 outbreak and its monetary implications for dental practices, hospitals and healthcare workers if the world fails to protect the economy, covid-19 will damage health not just now but also in the future coronavirus: drugs used to keep icu patients sedated end in four days in paraná, says secretary impact of coronavirus pandemic in appointments and anxiety/concerns of patients regarding orthodontic treatment how does the quarantine resulting from covid-19 impact dental appointments and patient anxiety levels? aerosol and surface stability of sars-cov-2 as compared with sars-cov-1 transmission of 2019-ncov infection from an asymptomatic contact in germany provides for the strategic action "brazil counts with me-health professionals", aimed at training and registering health professionals acute stress disorder, depression, and tobacco use in disaster workers following 9/11 presumed asymptomatic carrier transmission of covid-19 evaluation and treatment coronavirus (covid-19) covid-19 -navigating the uncharted how will country-based mitigation measures influence the course of the covid-19 epidemic? key: cord-000566-271vldil authors: lacerda, marcus vg; mourão, maria pg; alexandre, márcia aa; siqueira, andré m; magalhães, belisa ml; martinez-espinosa, flor e; santana filho, franklin s; brasil, patrícia; ventura, ana mrs; tada, mauro s; couto, vanja scd; silva, antônio r; silva, rita su; alecrim, maria gc title: understanding the clinical spectrum of complicated plasmodium vivax malaria: a systematic review on the contributions of the brazilian literature date: 2012-01-09 journal: malar j doi: 10.1186/1475-2875-11-12 sha: doc_id: 566 cord_uid: 271vldil the resurgence of the malaria eradication agenda and the increasing number of severe manifestation reports has contributed to a renewed interested in the plasmodium vivax infection. it is the most geographically widespread parasite causing human malaria, with around 2.85 billion people living under risk of infection. the brazilian amazon region reports more than 50% of the malaria cases in latin america and since 1990 there is a marked predominance of this species, responsible for 85% of cases in 2009. however, only a few complicated cases of p. vivax have been reported from this region. a systematic review of the brazilian indexed and non-indexed literature on complicated cases of vivax malaria was performed including published articles, masters' dissertations, doctoral theses and national congresses' abstracts. the following information was retrieved: patient characteristics (demographic, presence of co-morbidities and, whenever possible, associated genetic disorders); description of each major clinical manifestation. as a result, 27 articles, 28 abstracts from scientific events' annals and 13 theses/dissertations were found, only after 1987. most of the reported information was described in small case series and case reports of patients from all the amazonian states, and also in travellers from brazilian non-endemic areas. the more relevant clinical complications were anaemia, thrombocytopaenia, jaundice and acute respiratory distress syndrome, present in all age groups, in addition to other more rare clinical pictures. complications in pregnant women were also reported. acute and chronic co-morbidities were frequent, however death was occasional. clinical atypical cases of malaria are more frequent than published in the indexed literature, probably due to a publication bias. in the brazilian amazon (considered to be a low to moderate intensity area of transmission), clinical data are in accordance with the recent findings of severity described in diverse p. vivax endemic areas (especially anaemia in southeast asia), however in this region both children and adults are affected. finally, gaps of knowledge and areas for future research are opportunely pointed out. plasmodium vivax is the most geographically widespread species of plasmodium causing human disease, with most cases reported in central and southeast asia, in the horn of africa and in latin america [1] . it is considered to be a potential cause of morbidity and mortality amongst the 2.85 billion people living at risk of infection, excluding the large african populations who are mostly duffy negative and, therefore, naturally less susceptible to this infection. however recent data suggest that the parasite is evolving and may use alternative receptors other than duffy (darc) for erythrocyte invasion [2] . it is estimated that 5.5% of the population under risk live in the americas [3] . the major biological characteristic of this parasite is the presence of liver hypnozoites responsible for the frequent relapses, which add a substantial number of cases to the general burden of the disease, what is being faced as one of the most challenging bottlenecks for vivax malaria eradication [4] . although often regarded as causing a benign infection, there is recent increasing evidence that the overall burden, economic impact, and severity of p. vivax have been underestimated, in part due to a bias in the scientific literature which traditionally devoted most of its attention to the more lethal parasite plasmodium falciparum, probably as a reflection of a more substantial funding [5] . until 16 october 2011, the search in med-line using p. vivax as keyword retrieved 5,026 indexed abstracts; using p. falciparum, on the other hand, retrieved almost five times more abstracts: 25, 807 . even in places where p. vivax represents the major local problem to be tackled, clinical research is still focused on p. falciparum [6] . there is robust evidence in the past decade from hospital-based studies in india and indonesia that p. vivax is able to cause severe disease [7, 8] . some authors argue that this clinical severity may only now be properly recognized and announced by researchers in the field, but these complications apparently are not new from a historical perspective [9] . actually, the case fatality rate (cfr) related to malarial infections in the english marshes during the 16th and 17th centuries, corresponding to the little ice age, suggest that p. vivax (a parasite more prone to persist in vectors even under low temperatures) may have killed part of this population already victimized by famine [10] . during the first half of the 20th century, malariotherapy in patients with neurosyphilis, using essentially the 'nonsevere' p. vivax parasite, led to diverse complications, cfr ranging from 3.3 to 30.3% [11] . the major related complications in these co-infected patients were liver damage, ruptured spleen, jaundice, delirium, uncontrolled vomiting and persistent headaches [11] . that reinforces the concept that p. vivax infection may synergize with other co-morbidities resulting in more complicated disease. added to local geographical and social determinants, wide annual parasite incidence (api) and cfr variations due to this species are seen around the world. in summary, p. vivax, which has long been neglected and mistakenly considered 'benign' [12] , is receiving an increasing amount of importance in the debates taking place on malaria epidemiology and control, drug resistance, pathogenesis and vaccines [13] . as reviewed elsewhere, the good clinical characterization of severe disease in vivax infection is the first step to understand how the inflammatory response to this parasite contributes to pathogenesis [14] . traditionally, brazil has been responsible for almost half of all cases of malaria in latin america. in 2009, 308,498 cases of malaria were reported in this country (257,571 caused by p. vivax), representing 54.9% of all the malaria reported in the americas [15] . cases are virtually restricted to the amazon basin (constituted by the states of amazonas, acre, roraima, amapá, pará, tocantins, rondônia, and parts of mato grosso and maranhão). amazonian urban agglomerations under continuous economical development trigger intense migration flows, such as in the city of manaus (in the western brazilian amazon), helping to maintain the disease under endemic levels [16, 17] . malaria in brazil is mostly related to p. vivax since the 1990s, when the available tools for control at the moment were put together and intensified, such as the fast diagnosis through thick blood smear (tbs) in all febrile patients, and free access to anti-malarials, integrated through a decentralized primary care-centred public health system [18] . allied to that, an active community of local malariologists has been persistently identifying the profile of anti-malarial resistance with permanent counseling to the brazilian ministry of health, which responds promptly to these evidences, changing the first line regimens [19] . as the sexual forms (which are infective for the vector) of p. falciparum generally appear later in the course of infection, opportune diagnosis and treatment tend to have a high impact on reducing the transmission intensity of this species but the same is not true for p. vivax, whose gametocytes are present in the very first days of the infection, before efficacious treatment is usually started. in 2008, 59% of all malaria cases registered in the brazilian amazon were treated in the first 48 h after appearance of symptoms (sivep-malaria, 2009). these public health measures allied to a regularly updated online information system also impacted the number of deaths related to p. falciparum, which were not more than 58 in 2009 (brazilian ministry of health, 2010). as a consequence, even in the non-indexed literature, severity due to p. falciparum is not frequently reported anymore in brazil. brazil has reported 85% of its cases related to p. vivax in 2010, which puts this country in a peculiar epidemiological situation, as one of the few countries around the world with p. vivax predominance. the impact of p. vivax/p. falciparum co-infections or simultaneous circulation of both species with similar frequencies in a given population, upon the immunological status and clinical presentation of malaria is still unclear [20, 21] , but most probably clinical data from population from certain areas should not be extrapolated to other areas in distinct epidemiological conditions. actually, the lack of data on clinical presentation of p. vivax infection allied to the several particularities of this region, including the diverse genetic background of its population, implicate that the generalization of the findings from southeast asia may be inappropriate. in brazil, in 1903, the young physician carlos chagas (most known for the discovery of american trypanosomiasis afterwards) wrote his md thesis on the haematological complications of malaria, which, at that moment, also occurred in the non-amazon area. his major findings in studying p. vivax patients were severe anaemia, splenomegaly, leukopenia, cachexia and jaundice associated to concomitant staphylococcal disease [22] . bone marrows were also analysed in these patients with no conclusive findings. later on, during the 1940s, djalma batista in manaus described a series of malarial cases from his outpatient clinics in whom large splenomegaly, cachexia and minor bleeding were frequent among those with the 'benign' tertian malaria [23] . more recently, from 1998 to 2008, 234 deaths related to vivax disease were officially reported to the brazilian ministry of health [18] , and an increase in the hospitalization trends for vivax patients was published in a tertiary care hospital from manaus [24] . to complicate matters, these facts parallel a lack of robust biomarkers and specific criteria for severe disease for this species in the literature. a sine qua non requisite in the analysis of clinical severity related to p. vivax infection is the exclusion of mixed infection with p. falciparum through a more sensitive technique such as pcr and the exclusion of other co-morbidities which may be responsible for the clinical presentation per se. in the literature, in general, reports of 'complicated/severe' cases lack more precise and uniform definition criteria, in part due to the rare application of more robust endpoints such as death and admission to the intensive care unit (icu), and therefore end up suffering bias through individual judgment of authors, editors and reviewers. as in most of the data published there were no systematic exclusion of co-morbidities and/or mono-infection confirmation using pcr, performing a meta-analysis of severe manifestations of p. vivax becomes virtually impossible. the other bias in the case of brazil is that many relevant data are confined in abstracts from national scientific meetings and graduate students' dissertations and theses. the systematic review of these unpublished data therefore could contribute to the understanding of the clinical spectrum of vivax infection in this country and ultimately as a representative sample from latin american vivax malaria. the sources for published data on clinical aspects of vivax infection in brazil were medline (1948 to february 2011) and lilacs (1982 to february 2011). the following search strategy was devised for both databases: (plasmodium vivax).mp. and (brazil).mp. all types of study designs with primary data were included (cross-sectionals, case-controls, cohorts, case series and case reports). the abstracts were analysed in details by two independent reviewers and publications were selected if they mentioned any type of clinical complication (no specific criterion was used) in at least one patient with the diagnosis of vivax infection. disagreement between the two reviewers was solved through consensus. articles were excluded if they were reviews and also if they did not contain primary data on clinical aspects. for included studies, there were extracted data on date of publication, location, number of patients, and characteristics of participants (age range, pregnancy status, presence of co-morbidities), if molecular diagnosis through pcr was used to assess vivax malaria mono-infection and fatality. exclusion criteria for analysis were participants with mixed infections (p. falciparum/ p. vivax); studies in where patients with p. falciparum and p. vivax were both presented but the clinical data reported was not individualized for each species; and studies reporting the same patients from previous studies from the same authors. through abstract analysis, 297 articles were retrieved and after application of the inclusion and exclusion criteria, 27 articles (from 1987 to 2011) were selected, which are presented in table 1 . unpublished studies were searched manually in the annals of the congress of the brazilian tropical medicine society (published in supplements of the indexed journal revista da sociedade brasileira de medicina tropical [journal of the brazilian society of tropical medicine]), from 1964 to 2011. this is the most traditional scientific event for tropical medicine clinicians in brazil. similar inclusion and exclusion criteria were used in this search. however if the same abstract data were published afterwards as a full paper, the published paper information was presented here. if the abstract referred to a dissertation or thesis, this more detailed information was presented instead. forty-five abstracts were retrieved from 1995 to 2011. of these, 17 fulfilled any of the exclusion criteria and therefore, 28 abstracts are presented in table 2 . masters' dissertations and doctoral theses abstracts since 1987 were searched in the online database http:// capesdw.capes.gov.br/capesdw/teses.do maintained by the coordination for the improvement of higher education personnel (capes), the institution which coordinates and supervises all the brazilian graduate programmes in all areas of knowledge. the full original electronic documents were downloaded from the website when available or obtained through contact with the respective graduate students. ten dissertations and three theses are presented in table 3 . classical malaria paroxysms are typically short and sharply delineated within a period of less than eight hours. fever is one feature that is almost invariably present during a paroxysm. any of other common symptoms of the febrile syndrome, such as chills, rigours and sweating, are also described. these symptoms of a paroxysm could be accompanied by others, including headache, nausea and vomiting, and moderate to severe muscle, joint and back pain [93] . indeed high fever tends to be more evident in vivax disease even with lower parasitaemia, due to its recognized lower fever-threshold (around 100 infected rbcs/microlitre) [94] . therefore, any description of these classical symptoms, together or isolated, should be regarded by any experienced clinical as non-severe malaria, regardless of their intensity, because they are not associated to increased rates of hospitalization or fatality. in the brazilian literature reviewed, a wide spectrum of clinical complications aside from the classical symptoms of vivax malaria was found throughout the 68 indexed and non-indexed publications, despite the low number of deaths attributed to this species in this literature sample. the major complications are addressed as follows: world health organization (who) criterion for severe anaemia is haemoglobin below 5 g/dl in children and under 7 g/dl in adults. however the clinical manifestations due to anaemia per se are not known and to what extent it contributes to the respiratory distress associated with the hyperdynamic status of the febrile syndrome. there is scarce literature on malarial anaemia in population-based studies in latin america, as reviewed elsewhere [95] . on top of that, major differences in latin america are seen when the same methodology is applied. that is probably related to distinct genetic background and environmental factors, e.g. in the amazon basin (intense racial mixture) and in the colombian pacific coast (nonmixed black population) [96] . it is not known if anaemia is as frequent among patients from brazil as in southeast asian patients, where p. vivax is considered to be a disease of children because the acquisition of immunity against this species occurs much faster than for p. falciparum, in highly endemic areas [97] . in brazil only 25% of vivax disease affects children 0-14 years of age, however severe anaemia was reported in hospitalized children and adults, needing red blood cell (rbc) transfusions [45] . a key description of anaemia in vivax malaria children in latin america was published in venezuela in 2006 [98] . the 'congenital malaria' in newborns from the present series of reports with severe anaemia confirms previous findings that vivax malaria has an important clinical impact in children under 3 months [99] . non-severe anaemia, however, seems to be as frequent as 25.8% among the population of a recent occupation area in rondônia, where hydroelectric power plants are being built [100] . the cut-off of haemoglobin under 12 g/dl as a criterion of anaemia however should be seen with scepticism because of age ranges and the lack of baseline levels of haemoglobin validated to specific populations, which makes meta-analyses susceptible to misclassification. major confounding factors in the global analysis of anaemia are the local contributors to this haematological complication such as iron-deficiency anaemia, which was found to occur in 5.6% of a rural amazonian population, mostly among school children and women [101] . another important associated condition, which may interfere in the comparison between distinct populations, is the prevalence of intestinal helminthic infection. in a study performed with anaemic children, the presence of hookworms and malnutrition was cited [30] . however some controversy exists regarding this influence since in a cohort study, children with any intestinal helminth were protected from anaemia triggered by acute vivax infection [47] . in fact anti-helminthic treatment and iron supplementation reduced the haematological indexes in the population from an endemic area for malaria [102] . no brazilian study has addressed the concomitant diagnosis of parvovirus b19 as a contributing factor to anaemia in malaria, considering that recent evidence supports that the use of chloroquine (cq) may stimulate viral replication in the bone marrow, worsening anaemia [103] . apparently pregnant women develop anaemia as a major complication in vivax infection [32, 78] , and the impact upon the concept needs further investigation. chronic comorbidities affecting erythrocyte physiology, such as sickle cell anaemia (sca), may be related to more severe haemolysis and severe anaemia as well [40] . thrombocytopaenia as defined by platelet counts under 150,000/μl seems to be very frequent among patients with vivax malaria and apparently more frequent in vivax than in falciparum patients [104] , despite not being a consensus [105] . the increase in the report of thrombocytopaenia in several reference centres could also be a reflection of a better laboratorial infrastructure. only in recent decades in developing countries automated full blood counts included platelet count as a routine. many studies in brazil confirm that platelet counts are directly correlated to peripheral parasitaemia [89, 90] , but the meaning of this finding is still unknown. however, only mild bleeding is usually associated with this haematological complication in studies where detailed and systematic clinical description of the patients was made, even for severe thrombocytopaenia, which means in general platelet count under 50,000/μl [81, 89, 90] . in fact, there is no report in the whole literature of a fatal case of patient presenting exclusively with severe thrombocytopaenia, even for p. falciparum. that is probably why thrombocytopaenia, regardless of being described as a complication by who, is not strictly-speaking considered a severity criterion by itself [106] . what happens most of the time is that thrombocytopaenia is usually taken as a surrogate marker for dic in settings where no specific examinations to confirm this severe complication are available, such as prothrombin activation time, d-dimers and fibrin degradation products. however, there is a disproportionate difference in the proportions of thrombocytopaenia, which is considered relatively frequent in large studies for frequency estimation [90] and of dic, which is a rare complication, very scarcely reported in the literature associated to p. vivax infection [107, 108] . actually, there is some coagulation cascade activation, but usually with minor impact on coagulation tests and platelet counts [83] . it is important to consider however that in areas where dengue is also endemic, as is the case of brazil, thrombocytopaenia studies should obligatorily rule out this viral infection, which also presents a substantial percentage of thrombocytopaenia as part of its non-severe presentation [109] . in fact there are cases of co-infection already reported in the brazilian amazon recently [110] , but the literature poorly describes the clinical aspects of this coincidental infection [111] . respiratory distress is defined by oxygen saturation less than 94%, or deep breathing (acidotic breathing), or an age-stratified increased rapid respiratory rate (> 32/min in adults, > 40 in children 5-14 y, > 50 in children aged 2 mo to 5 y, and > 60 in babies less than 2 mo) [112] . however this syndromic approach does not translate any mechanism of disease and may be associated to the clinical presentation of febrile syndrome during the malarial paroxysm, severe anaemia, metabolic acidosis, lung oedema, pneumonia or acute respiratory distress syndrome (ards). in most of the cited brazilian studies, there are no described criteria on how respiratory distress was defined, which makes comparisons with the general literature impossible. sometimes imprecise clinical presentation is simply defined as pulmonary manifestations. in only one, ards is well characterized, comprising detailed radiological characterization and arterial gas analysis (fio 2 /pao 2 ) [37] . lung oedema is usually based on clinical and radiological parameters and the effect of fluid overload is not clear for vivax infection, since only a few cases were reported so far, brazilian cases included [39, 64, 65, 113, 114] . the impairment of respiratory symptoms after the beginning of treatment with cq referred elsewhere [115] was not mentioned in any of the present reports, which could be due to inappropriate study design. ruling out pneumonia is not easy because of the low frequency of positive blood cultures and due to the fact that in most of these patients with pulmonary complications empirical antibiotics are initiated as a rule. data from the papuan indonesia indicate that many infants who die with p. vivax have radiological evidence of pneumonia [116] , but the specificity of radiological findings to differentiate vivaxinduced pulmonary abnormalities from pneumonia is questionable. in mozambique, pyogenic bronchopneumonia was a common cause of respiratory distress in autopsied pregnant women with falciparum malaria, in both hiv positive and negative [117] . in the amazon, hiv prevalence is estimated to be~1% (unpublished data), which makes opportunistic diseases less prone to impact on severe clinical complications of vivax malaria, as is the case for falciparum malaria in africa. this is classically the most lethal clinical complication of severe falciparum malaria and the definition is also very imprecise with a wide spectrum of possible presentations, such as: impaired consciousness or unrousable coma (glasgow coma score ≤10 or blantyre coma scale ≤2); prostration, i.e. generalized weakness so that the patient is unable walk or sit up without assistance; failure to feed; or multiple convulsions (more than two episodes in 24 h). despite being infrequent in our studies, the phenomenon was also reported but not only in children [36, 86] . these reports must be very cautious in terms of ruling out other malarial complications as the cause of the neurological manifestations, such as hypoglycaemia and metabolic acidosis, but also associated infections as bacterial or viral meningoencephalitis. in india, acute intermittent porphyria was an unexpected co-morbidity associated to the neurological manifestations of patients with vivax malaria [118] . in papua, p. vivax-associated coma was rare, occurring 23 times less frequently than that seen with falciparum malaria, and was associated with a high proportion of non-malarial causes and mixed infections detected using pcr [119] . this complication is suspected in cases of oliguria and confirmed if serum creatinine is higher than 3.0 mg/dl. bacterial sepsis, dehydration, shock and past history of chronic renal failure should be routinely searched in the differential diagnosis. it was also reported in the brazilian literature [38, 48] , but in one study one case was found in a patient with arterial hypertension, what could be a triggering condition [45] . despite not being frequent in brazil, plasmodium malariae is found in some scattered areas [120] , and as a potential cause of glomerulonephritis [121] , this parasite should be ruled out by molecular biology tools whenever acute renal failure is detected in a malarial patient with vivax infection, due to similarities of these two species at routine optical microscopy. new who guidelines already point to hyperbilirubinaemia (total bilirubin > 3.0 mg/dl) as being a weak marker of severity, unless it is followed by any other vital organ dysfunction [106] . this finding seems to be the most frequent among children and adults with vivax disease considered as 'severe' [122, 123] . since haemolysis is not usually as severe as to cause significant clinical jaundice, most of these patients actually have some hepatocyte necrosis as evidenced by the mild to moderate liver enzymes (ast/alt) increase with subsequent cholestasis [124] . it was shown that icteric syndrome was a common cause of hospitalization in pregnant women with vivax malaria in manaus [87] . it was also detected in newborns [59, 74] , which makes vivax malaria an obligatory differential diagnosis of neonatal sepsis. jaundice in the presence of vomiting and upper abdominal pain should raise suspicion on acalculous cholecystitis, a poorly described complication apparently with good prognosis [125] . other diseases that may evolve to an icteric syndrome may be ruled out, especially because they are also more frequent in the tropics, such as leptospirosis [34] and typhoid fever [126, 127] . hepatitis a virus (hav) and vivax co-infection has already been reported as cause of jaundice and high elevation of transaminases [45] . hepatitis b virus (hbv) is also highly prevalent in brazil, especially in the amazon [128] and there is some evidence that p. vivax/hbv co-infection may be related to more frequent jaundice [80] and higher transaminase levels. algid malaria refers to the shock syndrome usually defined as circulatory collapse (systolic pressure under 70 mmhg in adults or under 50 mmhg in children) non-responsive to fluids. in the present vivax malaria reports, it was more reported most frequently among patients who died, suggesting that, as expected for this severe clinical complication, it could be regarded as a good marker of severity. however, the aetiology of this complication is still unclear even for p. falciparum. apparently it is multifactorial and the complication should be regarded as a syndrome where cardiac dysfunction, dehydration, bleeding, adrenal insufficiency, and bacterial sepsis could all play a role [129] . a review of all malaria deaths in the usa found that 5% were due to p. vivax associated with cardiac disease [130] , which suggests cardiac dysfunction as a contributing factor to algid malaria. there is robust evidence that bacteraemia in africa is associated with higher fatality in falciparum malaria in children [131] . less frequently shock occurs isolated, but usually as part of multi-organ dysfunction syndrome (mods), leading to a clinical picture suggestive of 'malaria-induced toxic shock' [132] . metabolic acidosis (plasma bicarbonate < 15 mmol/l) and hyperlactataemia (lactate > 5 mmol/l), which are common in severe falciparum malaria and are good predictors of fatal outcome, have never been described in vivax severe disease. in a series of children with vivax infection admitted to the icu, metabolic acidosis is mentioned [92] , however concomitant sepsis is described in this series and specificity for malaria cannot be assumed. if one admits lactic acidosis as a consequence of hypoxia triggered by microvasculature obstruction in falciparum disease, the scarcity of data on the frequency of this phenomenon in vivax disease may simply reflect the less severe obstruction due to less cytoadhesion, as already suggested elsewhere [133, 134] . in the case of hypoglycaemia (blood glucose < 40 mg/dl), the complication has been rarely described elsewhere [123, 135] , and in only two studies in brazil this finding was reported among children and pregnant women [32, 92] . the impact of vivax infection upon pregnancy and the concept is less clear in brazil and latin america as a whole, despite robust evidence that vivax malaria causes low birth weight and maternal anaemia exists in thailand [136] and indonesia [137] . the burden of the infection due to this species in brazilian pregnant women from a highly endemic area in the amazon seems to be high [138] . malaria anaemia in pregnant women with vivax is already known [137] and data from brazil confirm that this is the most common complication among these women [78] . additionally the few reports in the present series also point to low birth weight, vaginal bleeding, amniorrhexis, abortion, premature delivery, hypoglycaemia, hepatitis and jaundice as complications [31, 32, 49, 70, 87] . hyperemesis gravidarum may superimpose to the febrile syndrome and to the gastrointestinal side effects associated to cq in pregnant women, contributing to uncontrolled vomiting and consequent metabolic disorders. apparently in the case of pregnancy, co-morbidities do not seem to be frequent among patients with clinical complications. despite the need of more pathogenesis studies with the infected placenta, ultrasound studies in order to search for prognostic markers are urgently needed. some atypical complications are not frequently described for malaria and likewise are not classically referred as severe malaria. rhabdomyolysis has been reported for vivax in 1993 in a patient with myoadenylate deaminase deficiency [139] ; only one case was reported in brazil in a patient without co-morbidities [46] . rarely, patients with vivax malaria could evolve with immune thrombocytopenic purpura (itp) as a complication of the acute infection [33] . to confirm this diagnosis, the patient has to be followed up with persistent thrombocytopaenia for many weeks after the efficacious anti-malarial treatment and diseases, in which itp is more frequently seen, such as hiv, should be discarded. the mechanisms involved are poorly understood. splenomegaly is considered a typical finding in the physical examination of a patient with vivax disease, but the occurrence of spleen haematomas evolving with rupture and fatal outcome is relatively rare [41, 52, 91] despite being more frequent among this species as compared to falciparum [140] . in any case, patients with vivax malaria referring abdominal pain should be investigated for this complication as some patients may evolve with a bad prognosis if not properly managed by a surgeon. ocular manifestations in vivax disease apparently have no relation to cerebral malaria or bad prognosis, as is the case for falciparum [141] . few reports have been published on vivax patients with non-severe disease and retinal haemorrhage [142] and in brazil this fundoscopical finding was associated with hypovitaminosis a [35] . another atypical complication, which may be more frequent than expected for vivax infection, and with outstanding impact upon the development of some emerging economies in the globe, is poor school performance which should be a surrogate marker for the intellectual impairment related to malaria [143] . acute malnutrition has been shown to be a complication of vivax malaria in highly endemic areas [144] . in brazil a few evidences show that malnourishment and vivax co-exist but the impact of this association is still unknown [145] . in only two studies was malnutrition referred to as a possible cause of the reported clinical complication [92, 146] . vasculitis [66] , leukemoid reaction [76] and pleural effusion [62] as a marker of severity seems to be speculative and details of these reports do not support any in-depth analysis. high parasite density as a marker of severity for p. vivax, as it is for p. falciparum, still needs additional studies, considering this parasite infects preferably reticulocytes. the same occurs with the presence of schizonts in peripheral blood, which is usually associated with high sequestered biomass and severity for falciparum [147] , but is still an unexplored aspect for vivax. strong linear trends were identified regarding increasing plasma levels of c reactive protein (crp) and the gradation of disease severity [48] . super-oxide dismutase-1 (sod-1) seems to be a powerful predictor of disease severity in individuals with different clinical presentations of vivax malaria [148] . as soon as precise markers of severity are available, it would be possible to design studies powered to analyse the influence of the host genetics in the development of severe vivax disease. some association between pulmonary manifestations and tnf and il-12 polymorphisms has been attempted [79] . it has been proposed for the first time in manaus that g6pd deficiency could protect against vivax malaria, in a cross-sectional study, based on past history of the enrolled population [149] . this protection was later confirmed in pakistan [150] . male hemizygotes for this deficiency also showed to be protected against severe falciparum malaria [151] . no data exist on the protection against severe vivax disease. likewise, people with the fya/fyb genotype presented higher susceptibility to clinical vivax malaria [152] . since the discovery in brazil that duffy-negative individuals could be infected by p. vivax [153] , some speculation on the other possible invasion receptors has emerged. however, cohort studies are needed to investigate the real impact of the distinct duffy genotypes on clinical malaria incidence, submicroscopic asymptomatic infection, malaria-triggered anaemia and lower parasitaemia, as already suggested for fyb/fyx and fya/fyx genotypes in the brazilian amazon [154] . the major advance in the study of the pathogenesis of severe vivax disease was the demonstration of p. vivaxinfected rbcs cythoadhesion on human lung endothelial cells (hlec) and placental tissue ex vivo [134] . this cythoadhesion was obviously lower than p. falciparuminfected rbcs adhesion, but with similar stability. however the next challenge is to try to link this finding to the in vivo phenomena [155] . the increased adhesion with the addition of lps in the p. vivax ex vivo model suggests that endothelial activation may be an enhancing event. the role of augmented platelet-derived microparticles [156] and cd4 + cd25 + foxp3 + regulatory t cells (tregs) cells found in vivax disease should also be investigated in severe disease. plasma levels of tnf, ifn-γ and also ifn-γ/il-10 ratios were increased and exhibited a linear trend with gradual augmentation of disease severity [48] . patients with severe disease also presented higher haemolysis and higher plasma concentrations of cu/zn sod-1 and lower concentrations of pge-2 and tgf-β than those with mild disease [157] . oxidative stress was also proposed as a mechanism for thrombocytopaenia found in vivax disease [158, 159] , as well as its association with tnf [85] . circulating immune complexes were not associated to vivax thrombocytopaenia [89] , but polymorphisms of the highly immunogenic ama-1 were associated to platelet count in these patients [160] , suggesting that immunological mechanisms are involved in platelet destruction. in the case of anaemia, there is no correlation between the presence of anti-erythrocyte and anti-cardiolipin antibodies and the presence or intensity of this haematological finding [161] . auto-immunity induced by secondary cryoagglutinins should be explored [54] . erythropoiesis seems to be affected [162] , and the finding of parasites inside the bone marrow [43] stimulate the search for mechanisms of diserythropoiesis in this milieu, despite technical limitations to analyse this tissue in humans. the role of the spleen in severe disease is still unknown, as well as the role of the variant subtelomeric multigene vir family, which may influence the sequestration of infected rbcs in this organ [163] . parasite genetics, such as msp-1 and csp polymorphisms, has not been shown to be associated with clinical severity [164] . in summary, the immune response in patients with severe vivax disease has not been fully addressed in the general literature, and further approaches are needed in order to unveil immune mechanisms related to these complications. in terms of therapy, cq and primaquine (pq) are still the drugs of choice for the treatment of vivax malaria in many endemic areas, brazil included. it is important however to keep in mind that side effects of these drugs could be erroneously taken as clinical severity associated to the parasite infection. in the case of cq, it is considered a safe drug, despite the occurrence of pruritus, which most of the time is considered to be a minor effect and rarely requires the drug withdrawal [165] . psychosis on the other hand is a more severe complication [75, 166] , as well as cardiac arrhythmia [29] . atypical complications of its use such as severe gastric bleeding were associated with haemophilia a [50] . in the case of pq, tranquillity is not the same as with cq, because pq is able to induce metahaemoglobinaemia [42, 51] and severe haemolysis [44] in patients with g6pd deficiency. the burden of the deficiency in brazil is poorly measured but the few data available in endemic areas for malaria has shown it to be between 3.0% [149] and 5.8% [167] among men, since the deficiency is linked to the x-chromosome. in the case of brazil, the prescription of pq in the abbreviated regimen (0.5 mg/kg/day for 7 days) without any routine g6pd screening may contribute to increase the frequency and severity of the side effects triggered by this drug, as confirmed by the reports of patients with blackwater fever after pq use, including one fatal case [63, 71, 91, 92, 168] . to complicate matters, for the radical cure, the new drug under late stage clinical investigation, tafenoquine, shows no evidence that it is safer than pq in g6pd deficient [169] . the simultaneous occurrence of severe vivax disease and cq-resistance in some countries has raised the question of a possible association between severity and resistance, especially for anaemia [170] . cq resistance actually has been reported in brazil almost at the same time as clinical severity [171, 172] , but some studies argue against that, showing that severe patients responded to cq [45] . added to that, reliable genetic markers of resistance are lacking [173] . increased levels of pvmdr-1 and pvcrt-o rna in a single severe patient with vivax malaria however paved the way to the study of gene expression in association to resistance [174] . as suggested by the present data, 11 cases were reported in brazilian travellers who live in the non-endemic area and occasionally go to the amazon. regarding the possibility of severe disease triggered by p. vivax, travel outpatient clinics should emphasize to their clients the possible complications of this disease, still considered 'benign' in most of the educational folders and travellers' guides, especially because no good chemoprophylaxis against relapses related to this species is available to date. on top of that, retarded diagnosis and treatment outside the amazon area contributes to the higher fatality rate of p. falciparum patients [18] . a similar situation could be observed for p. vivax, being this disease misdiagnosed as other febrile diseases. despite the increasing evidence of cq-resistance worldwide, the brazilian ministry of health still recommends cq as the first line therapy for vivax treatment, considering that only one single study has properly shown~10% of resistance in the area of manaus [172] . the few available efficacy studies on act for the treatment of vivax were reviewed recently [175] , and give good evidence for their use in vivax malaria, however, more studies are needed. only recently the brazilian ministry of health followed the who recommendations to manage vivax severe patients with parenteral artemisinin derivatives as if they had severe falciparum infection, considering that a submicroscopic mixed infection could be misdiagnosed in the routine tbs [106] . this recommendation was already stated by the famous brazilian parasitologist samuel pessôa in his medical parasitology textbook, from 1967 [176] . supportive therapy is even more neglected and there is virtually no study focusing in the clinical management of patients with severe vivax disease. there are actually many priorities in clinical research related to vivax disease. the major ones were discussed previously. considering that asymptomatic infections due to p. vivax are even more common in endemic areas for both species [177] , the likelihood of an asymptomatic patient becoming ill due to another microorganism is not improbable, which requests a good epidemiological characterization of the endemic area where the severe cases are being reported and systematic exclusion of mixed infections through pcr, due to the possibility of submicroscopic infection with p. falciparum. another major priority in vivax research is the investigation of concurrent infections through systematic laboratory exclusion of the most prevalent infectious diseases in severe patients. in figure 1 , the major research questions are addressed. in the present systematic review, the major limitation was the fact that most of the information was retrieved from non-peer reviewed sources. however, it seems clear that vivax patients in brazil are calling the attention of their physicians only recently. like other infectious diseases, defining severity criteria is a major challenge. as an example, dengue fever specialists have defined 'warning signs' for dengue haemorrhagic fever, the most lethal complication of the infection due to dengue virus, which are early signs that should raise the suspicion of severe dengue but are not applied themselves to the final classification [178] as proper intervention can avoid the patient evolving to more severe stages. sometimes in the literature potential 'warning signs' for severe vivax malaria are mistaken for severity criteria, which are those ultimately related to increased fatality. who severity criteria formerly developed for falciparum disease seem to apply reasonably to vivax disease as well, but there are clearly 'warning signs' that should motivate clinicians from the tropics to observe patients more closely, such as isolated thrombocytopaenia, isolated jaundice or the presence of chronic or acute co-morbidities. for example, during influenza outbreaks, the virus does not necessarily kill per se, but compromises the most vulnerable population and facilitates fatal secondary bacterial infections. the most common complications observed in the field are not necessarily the most frequently reported in the literature, sometimes biased by the uniqueness or exoticness of the cases reported. it is only after 1987 that these cases started to be reported in brazil in indexed and nonindexed publications, which may simply parallel the increase in the absolute numbers of vivax cases in brazil, culminating in the more frequent observation of rare clinical events triggered by this parasite. publication bias may also impact the chronology of these complicated case reports, especially when research group leaderships based in the endemic areas start to look for clinical aspects more closely. it is noteworthy however that studies on pathogenesis must be careful when dealing with severe vivax disease as a single entity. the best approach is to study groups of patients with specific complications (e.g., severe anaemia or ards) in order to minimize the risk of heterogeneous groups with probable multifactor causality, including the diversity of host genetics. the amount of complications related to anti-malarial drug use is not negligible, especially primaquine. multicentric studies using standard protocols, with the proper care of confirming mono-infection by more specific tools (e.g. pcr) and ruling out co-morbidities, are urgently needed to characterize the real spectrum of vivax disease worldwide. tissues from deceased patients are also waited, in order to support more robust analyses of the mechanisms of death. without that information, vaccine clinical trials against p. vivax will not be able to include among their endpoints the protection against the severe disease (essentially severe anaemia), which parallels the frequency of severe falciparum anaemia in some endemic areas. the recent discussion on malaria eradication will only succeed if the two parasites which most affect humans begin to be treated as distinct and not causing a single disease. clinical characterization is the first step to estimate its burden and ultimately to plan any control strategy in the near future. the neglected burden of plasmodium vivax malaria duffy negative antigen is no longer a barrier to plasmodium vivax-molecular evidences from the african west coast (angola and equatorial guinea) the international limits and population at risk of plasmodium vivax transmission in 2009 key gaps in the knowledge of plasmodium vivax, a neglected human malaria parasite vivax malaria: neglected and not benign the neglected plasmodium vivax: are researchers from endemic areas really concerned about new treatment options? plasmodium vivax malaria multidrug-resistant plasmodium vivax associated with severe and fatal malaria: a prospective study in papua severe vivax malaria: newly recognised or rediscovered from shakespeare to defoe: malaria in england in the little ice age the history of malariotherapy for neurosyphilis. modern parallels is plasmodium vivax still a paradigm for uncomplicated malaria? plasmodium vivax: who cares? defying malaria: fathoming severe plasmodium vivax disease urban expansion and spatial distribution of malaria in the municipality of manaus, state of amazonas non-planed urbanization as a contributing factor for malaria incidence in manaus-amazonas malaria in brazil: an overview chemoresistance of plasmodium falciparum and plasmodium vivax parasites in brazil: consequences on disease morbidity and control plasmodium vivax and mixed infections are associated with severe malaria in children: a prospective cohort study from papua new guinea the interaction between plasmodium falciparum and p. vivax in children on espiritu hematological studies of impaludism the paludisme in the amazon: a contribution to epidemiology, protozoology and clinics, study about the billiary-hemoglobinuric fever malaria diagnosis and hospitalization trends respiratory manifestations in plasmodium falciparum and vivax malaria neonatal malaria: report of a case laboratory profile of malarial patients congenital malaria: case reports and brief review of literature chloroquine and cardiac arrhythmia: case report plasmodium vivax malaria in children and adolescents -epidemiological, clinical and laboratory features malaria during the pregnancy and low birth weight from endemic areas in the amazon malaria in pregnant women of a public maternity of rio branco (acre state, brazil) idiopathic thrombocytopenic purpura due to vivax malaria in the brazilian amazon severe sepsis due to severe falciparum malaria and leptospirosis co-infection treated with activated protein c serum vitamin a levels in patients with ocular lesions attributable to non-complicated malaria in the brazilian amazon region cerebral malaria in ceara: a case report acute respiratory distress syndrome due to vivax malaria: case report and literature review report of a case of acute renal failure in plasmodium vivax malaria noncardiogenic pulmonary edema during vivax malaria malaria and sickle cell anemia: report of complications and clinical management of three patients in a highly endemic area for plasmodium vivax malaria in the brazilian amazon splenic hematoma in a patient with plasmodium vivax malaria association of methemoglobinemia and glucose-6-phosphate dehydrogenase deficiency in malaria patients treated with primaquine chronic plasmodium vivax infection in a patient with splenomegaly and severe thrombocytopenia clinical aspects of hemolysis in patients with p. vivax malaria treated with primaquine, in the brazilian amazon severe plasmodium vivax malaria, brazilian amazon. emerg infect dis severe rhabdomyolysis caused by plasmodium vivax malaria in the brazilian amazon concurrent helminthic infection protects schoolchildren with plasmodium vivax from anemia severe plasmodium vivax malaria exhibits marked inflammatory imbalance impact of malaria during pregnancy in the amazon region hypovolaemic shock triggered by p. vivax infection in a patient with mild haemophilia a methemoglobinemia in patients with plasmodium vivax receiving oral therapy with primaquine splenic rupture in malarial patients from the instituto de medicina tropical de manaus severe malaria in patient with plasmodium vivax infection: a case report hemolytic anemia due to secondary cryoagglutinins and p. vivax malaria: report of two cases thrombocytopenic purpura in patient with plasmodium vivax malaria: case report spontaneous splenic rupture in vivax malaria clinical and hematological profile of hospitalized patients with vivax malaria and thrombocytopenia in the fundação de clinical and laboratorial study on plasmodium vivax malaria neonatal malaria due to plasmodium vivax in the fundação de medicina tropical do amazonas death due to p. vivax in a non-endemic area thrombocytopenia in patients with plasmodium vivax malaria severe malaria due to p. vivax: case report the relevance of clinical and laboratorial aspects in patients with plasmodium vivax malaria hospitalized in the fundação de medicina tropical do amazonas patient with vivax malaria and acute lung edema in the brazilian amazon: case report and literature review severe vivax malaria and noncardiogenic pulmonary edema vivax malaria and vasculitis: case evolving with death splenic subcapsullary hematoma in patient with plasmodium vivax malaria case report: pulmonary manifestations of plasmodium vivax malaria malarial coma due to plasmodium vivax effects of malarial infection on the course of pregnancy and fetus in patients from the fundação de medicina tropical do amazonas hemolysis associated to acute renal failure in an immunocompetent patient with g6pd deficiency and vivax malaria: case report with favourable evolution severe malaria due to plasmodium vivax: case report evaluation of splenic immune response in patient infected with plasmodium vivax clinical manifestations of congenital vivax malaria in the western brazilian amazon acute psychosis induced by chloroquine during vivax malaria treatment leukemoid reaction caused by plasmodium vivax: case report the lung in vivax malaria: case report prevalence of anemia and plasmodium vivax infection in routine antenatal attention in a primary care center in the city of manaus pulmonary manifestations in patients infected with plasmodium vivax and correlation with tnf-alfa and il-12 polymorphisms clinical and laboratorial characteristics of human malaria and hepatitis b virus association clinical aspects, resistance and parasitary polymorphism of plasmodium vivax malaria in manaus malaria in pará: study of the clinical and laboratorial picture in infections caused by plasmodium vivax hemostasis disturbances in patients with malaria hematological characterization of children with vivax malaria diagnosed and treated in the fundação de medicina tropical do amazonas vivax malaria: clinical and laboratorial manifestations related to tnf-alpha master dissertation university of brasília, tropical medicine deprtment study of malaria in pregnant and puerperal women in a public maternity in manaus from clinical and epidemiological study of plasmodium vivax malaria in the state of amapá clinical manifestations and pathogenesis of malarial thrombocytopenia evaluation of frequency and factors associated to thrombocytopenia caused by plasmodium vivax study of 17 cases of autopsies from patients with the diagnosis of vivax malaria in a reference center in the brazilian amazon children under 14 years with malaria admitted to intensive care units in the brazilian amazon: a case-control study with plasmodium vivax patients the paroxysm of plasmodium vivax malaria why do we need to know more about mixed plasmodium species infections in humans? malaria-related anaemia: a latin american perspective comparative hematologic analysis of uncomplicated malaria in uniquely different regions of unstable transmission in brazil and colombia the risk of malarial infections and disease in papua new guinean children anemia and thrombocytopenia in children with plasmodium vivax malaria vivax malaria: a major cause of morbidity in early infancy malaria and hematological aspects among residents to be impacted by reservoirs for the santo antonio and jirau hydroelectric power stations anemia and iron deficiency in school children, adolescents, and adults: a community-based study in rural amazonia anaemia, iron deficiency and malaria in a rural community in brazilian amazon parvovirus b19 infection contributes to severe anemia in young children in papua new guinea thrombocytopenia in plasmodium falciparum, plasmodium vivax and mixed infection malaria: a study from bikaner (northwestern india) thrombocytopenia in malaria: who cares? guidelines for the treatment of malaria a case of plasmodium vivax malaria with findings of dic dic in vivax malaria thrombocytopenia in patients with dengue virus infection in the brazilian amazon concurrent dengue and malaria in the amazon region concurrent dengue and malaria who: severe falciparum malaria pulmonary edema due to plasmodium vivax malaria in an american missionary pulmonary oedema in vivax malaria acute lung injury and other serious complications of plasmodium vivax malaria the pathophysiology of vivax malaria an autopsy study of maternal mortality in mozambique: the contribution of infectious diseases acute attack of aip (acute intermittent porphyria) with severe vivax malaria associated with convulsions: a case report coma associated with microscopy-diagnosed plasmodium vivax: a prospective study in papua how prevalent is plasmodium malariae in rondonia, western brazilian amazon? delayed diagnosis of malaria in a dengue endemic area in the brazilian extra-amazon: recent experience of a malaria surveillance unit in state of rio de janeiro clinical features of children hospitalized with malaria-a study from bikaner, northwest india severe plasmodium vivax malaria: a report on serial cases from bikaner in northwestern india malarial hepatitis acute acalculous cholecystitis complicating an imported case of mixed malaria caused by plasmodium falciparum and plasmodium vivax mixed infection with plasmodium vivax and salmonella typhi in an infant concurrent salmonella bacteremia in p. vivax infection-a report of 2 cases at the hospital for tropical diseases natural history of chronic hepatitis b algid malaria: a syndromic diagnosis malaria deaths in the united states: case report and review of deaths, 1979-1998 severe malaria and concomitant bacteraemia in children admitted to a rural mozambican hospital two cases of plasmodium vivax malaria with the clinical picture resembling toxic shock lung injury in vivax malaria: pathophysiological evidence for pulmonary vascular sequestration and posttreatment alveolarcapillary inflammation on the cytoadhesion of plasmodium vivax-infected erythrocytes clinical and laboratory findings of plasmodium vivax malaria in colombia effects of plasmodium vivax malaria in pregnancy adverse pregnancy outcomes in an area where multidrug-resistant plasmodium vivax and plasmodium falciparum infections are endemic malaria during pregnancy in a reference centre from the brazilian amazon: unexpected increase in the frequency of plasmodium falciparum infections rhabdomyolysis associated with malaria tertiana in a patient with myoadenylate deaminase deficiency nonoperative treatment of splenic rupture in malaria tropica: review of literature and case report a review of the spectrum of clinical ocular fundus findings in p. falciparum malaria in african children with a proposed classification and grading system retinal hemorrhage in plasmodium vivax malaria malaria is associated with poor school performance in an endemic area of the brazilian amazon plasmodium vivax: a cause of malnutrition in young children the malarial impact on the nutritional status of amazonian adult subjects plasmodium vivax malaria in children and adolescents -epidemiological, clinical and laboratory features relation of the stage of parasite development in the peripheral blood to prognosis in severe falciparum malaria plasma superoxide dismutase-1 as a surrogate marker of vivax malaria severity glucose-6-phosphate dehydrogenase deficiency in an endemic area for malaria in manaus: a cross-sectional survey in the brazilian amazon the impact of phenotypic and genotypic g6pd deficiency on risk of plasmodium vivax infection: a case-control study amongst afghan refugees in pakistan x-linked g6pd deficiency protects hemizygous males but not heterozygous females against severe malaria duffy blood group gene polymorphisms among malaria vivax patients in four areas of the brazilian amazon region plasmodium vivax infection among duffy antigen-negative individuals from the brazilian amazon region: an exception? fy polymorphisms and vivax malaria in inhabitants of amazonas state on cytoadhesion of plasmodium vivax: raison d'etre? augmented plasma microparticles during acute plasmodium vivax infection heme impairs prostaglandin e2 and tgf-beta production by human mononuclear cells via cu/zn superoxide dismutase: insight into the pathogenesis of severe malaria oxidative stress of platelets and thrombocytopenia in patients with vivax malaria the role of platelet and plasma markers of antioxidant status and oxidative stress in thrombocytopenia among patients with vivax malaria martins braga e: association between particular polymorphic residues on apical membrane antigen 1 (ama-1) and platelet levels in patients with vivax malaria similar cytokine responses and degrees of anemia in patients with plasmodium falciparum and plasmodium vivax infections in the brazilian amazon region blood and bone marrow changes in malaria plasmodium vivax and the importance of the subtelomeric multigene vir superfamily molecular epidemiology of plasmodium vivax in the state of amazonas frequency of pruritus in plasmodium vivax malaria patients treated with chloroquine in thailand chloroquine-induced recurrent psychosis bonini-domingos cr: incidence evaluation of glucose-6-phosphate dehydrogenase and hematological profile in rondônia clinical and laboratorial alterations in plasmodium vivax malaria patients and glucose-6-phosphate dehydrogenase deficiency treated with primaquine at 0.50 mg/kg/day randomized trial of 3-dose regimens of tafenoquine (wr238605) versus low-dose primaquine for preventing plasmodium vivax malaria relapse new developments in plasmodium vivax malaria: severe disease and the rise of chloroquine resistance plasmodium vivax resistance to chloroquine (r2) and mefloquine (r3) in brazilian amazon region chloroquine-resistant plasmodium vivax, brazilian amazon. emerg infect dis analysis of single-nucleotide polymorphisms in the crt-o and mdr1 genes of plasmodium vivax among chloroquine resistant isolates from the brazilian amazon region increased expression levels of the pvcrt-o and pvmdr1 genes in a patient with severe plasmodium vivax malaria artemisinin combination therapy for vivax malaria rio de janeiro: guanabara-koogan high prevalence of asymptomatic plasmodium vivax and plasmodium falciparum infections in native amazonian populations understanding the clinical spectrum of complicated plasmodium vivax malaria: a systematic review on the contributions of the brazilian literature we acknowledge the organizers of the 47th congress of the brazilian society of tropical medicine, held in natal (rio grande do norte) on 23-26 march, 2011, especially its president dr. kleber luz, for embracing and supporting the 1st brazilian workshop on severe p. vivax as part of its official programme, from whose reflections this review was written. 1. what is the real incidence of severe disease in populationbased studies in latin america? 2. is the incidence of severe disease similar in distinct epidemiological scenarios? and what is the impact of the health system organization on this severity? 3. what is the prognosis and fatality rate of severe disease in hospitalized and non-hospitalized patients? 4. what is the role of host genetics (e.g. duffy genotypes, g6pd deficiency) upon severity? the authors declare that they have no competing interests. key: cord-353019-7wj0eu1f authors: alcadipani, rafael title: pandemic and macho organizations: wakeup call or business as usual? date: 2020-05-13 journal: gend work organ doi: 10.1111/gwao.12466 sha: doc_id: 353019 cord_uid: 7wj0eu1f the covid‐19 pandemic is one of the greatest challenges for our generation. the global spread of the virus is affecting societies’ gender dynamics in general and in organizations in particular. based on ethnographic research being carried out in a police organization in brazil, this piece discusses how covid‐19 is impacting hegemonic masculinity in organizations. police organizations are prototypical hegemonic masculinity organizations. i argue that the covid‐19 pandemic at first encourages the performance of the police typical macho masculinity, but as the disease progresses, it creates a situation that challenges it. i explore that even though the pandemic threatens macho masculinity in organizations, it is still unclear if an alternative gender dynamic will emerge from this crisis in macho organizations. different world leaders are positing covid-19 as the greatest challenge of our time. the effects on people's lives are immense and profound as covid-19 is impacting one of the central core stones of all human societies: social interaction. it is also affecting the economy and a myriad of taken for granted assumptions in our lives. it has changed our lives very rapidly and it still unclear how the world will emerge once the covid-19 situation is under control. the covid-19 pandemic is affecting gender dynamics and bringing gender gaps to the surface in many societies. the pandemic has been surrounded by a macho discourse of war all over the world. in some places, domestic violence against women is on the rise. besides, while many are being forced to work from home, the uneven distribution of care work between men and women becomes more evident (e.g. care of the elderly and homeschooling young children). however, at the same time new forms of gender and inter-gender solidarity are emerging making the covid-19 pandemic an important time for gender-related research. if, on the one hand, the pandemic affects minorities and the vulnerable more seriously, it can also have impacts on the performance of macho dominated organizations. i realize this due to ethnographic fieldwork that i have been carrying out in a police force in brazil. police officers, a highly hegemonic masculine group, are one of the key front-line workers in this pandemic. as a result, they are also suffering high levels of covid-19 contamination, some of which have resulted in death. to raise some questions concerning covid-19 and hegemonic masculinity, i am writing this piece to shed lights on how covid-19 is impacting hegemonic masculinity performances in organizations. i am calling this an opinion piece because i would like to share my impressions of covid-19 and hegemonic masculinity in these rather uncertain times. most of the studies on gender in the police have focused on women and "little is known about men's experience of policing through a gendered lens as men or through a theoretical lens of masculinity" (silvestri, 2017:03) . this article is protected by copyright. all rights reserved. to reflect on the impacts of covid-19 on masculinity, first i discuss that the police is a prototypical hegemonic masculine organization. then, i discuss how covid-19 is impacting the ethnographic fieldwork i have been carrying out in the police in brazil and also how to keep doing research in a pandemic. later, i discuss how the police macho masculinity has been displayed in the pandemic to later show how covid-19 threatens police macho masculinity. finally, i argue that the pandemic situation is potentially putting in danger macho masculinity in organizations, however, i also hypothesize that it is still unclear if the covid-19 will give place to alternative gender dynamics in organizations. writing this piece has been important to understand and also to deal with several threats covid-19 poses to all of us. the pandemic vanishes away any possibility of knowing what will happen to us, to our loved ones and also to society. seeing the hundreds of deaths every day by covid-19 makes our finitude even more salient and transparent. social isolation makes more difficult to provide care to our elderly parents. furthermore, i am facing this disease from brazil where the far-right proto-fascist president is possible one of the worst world leaders responding to this pandemic. he defies social isolation publicly almost every day, and every week he takes part in public demonstrations against the already fragile brazilian democracy. bolsonaro, the brazilian president, is the typical 'tough and forceful' macho who thinks he knows it all, that problems can be solved by public displays of strengths and by farright bravados. when asked by journalists about the covid-19 increasing death toll, bolsonaro replied: "so what?". he shows no solidarity to people at all and is a macho role model of careless and stupidity. brazil is one of the most unequal countries in the world and social isolation is an impossibility to most of poor brazilians, be it due to lack of adequate housing and sanitation, be it due to the need to work, sometimes making delivery of goods and services to the rich. there are reports that poor woman who works for providing care for the rich are the most susceptible to die from the virus in brazil. i think writing this piece in these this article is protected by copyright. all rights reserved. extraordinary times is a way to challenge macho masculinity in organizations and also to process all the rash environment we face in brazil. research on masculinities and organizations (e.g. ackroyd & crowdy, 1990; alcadipani & tonelli, 2014; cheng, 1996; collinson & hearn, 1996; collinson & hearn, 1994; collinson & hearn, 1996; kerfoot & knights, 1998; knights & kerfoot, 2004; pullen & knights, 2007; knights & clerke, 2017) analyzes mainly how problematic performances of masculinities aids in the perpetuation of institutional inequalities and violence and, hegemonic masculinity is rather present in governing work organizations (knights & pullen 2019) . in so doing, the concept of hegemonic masculinity has been crucial in the development of studies of masculinities in organizations (collinson & hearn, 1994; knight & tollberg, 2012) . the term hegemony comes from gramsci (see donaldson, 1993) and hegemonic masculinity signifies a "culturally idealized form of the masculine character" (connell, 1993) . this is the conventional dominant form of masculinity constructed in opposition to femininities and related to other subordinated, marginalized, and colonized modes of masculinities (connell, 1987; connell & messerschmidt, 2005) . forms of masculinities can be seen as stemming from power relations and can be characterized as either hegemonic or subaltern in relation to one another (collinson & hearn, 1994) . i depart from the view that gender is continuously performed (knights & tollberg, 2012) and i depart from the assumption that masculinities must be accomplished, they are not static (connell & messerschmidt, 2005; knights, 2019) . masculinities are therefore in a constant process of being constructed in specific social situations, reproducing or changing social structures (messerschmidt, 1993; connell, 1993) . organizations are an important setting for the achievement and performance of masculinities (cheng, 1996; collinson & hearn, 1996; kerfoot & knights, 1998; ackroyd & crowdy, 1990) as well as where hegemonic masculinities can be challenged (peukert, 2017) . historically, hegemonic masculinity has been strongly tied to social institutions such as the family, religion, and work (connell, 1993) . similar to the military (karazi-presler, 2020; lee et al., 2019) and fire departments (perott, 2019), hegemonic masculinity is distinctively prevalent in police organizations (see o'neill, mars & singh, 2007) . this makes police organizations an "overwhelming masculine institution" (willis, 2013:80) where the cult of masculinity is the defining characteristic of the police occupational culture (fielding, 1994; smith & gray, 1985) , even though there are places of resistance (dick, 2015) . police occupational culture has been portrayed as essentially masculine "with an emphasis on virility, toughness, masculinity, and masculine interests such as sexual triumphs, sports, outdoor life, and so forth" (van maanen & manning, 1978: 249) . specifically, police officers self-perceived themselves as masculine heroes who take all danger to fight crime (manning, 1977) and are typically male, white and heterosexual (foster, 2003) , assuming a taken for granted heterosexual masculinity (loftus, 2008) in which homosexuality is perceived as deviance (burke, 1993) . since the police academy, police officers are in contact with a hidden curriculum teaching hegemonic masculinity to novices (prokos & padavic, 2002) . physical displays of masculinity and the bravery to face danger, is a central characteristic that defines the "macho" police officer (crank, 2004; dick & cassell, 2004; young, 1991) . another important element of police occupational culture is a masculine favoring of reason over emotion (fassin, 2013) which can even play down stress in everyday police work (yates, riach & johansson, 2017) . the cult of masculinity is performed, for example, in police storytelling within the organization making a natural feature the use of violence and force when facing "bad-guys" (dick, 2005) and also the need to prove their masculinity in daily work (wilson, 1968) . these this article is protected by copyright. all rights reserved. stories construct the (macho) heroic police identity (bayley, 1994; van maanen, 1980) . the masculine body in terms of physical strength is perceived as the main tool the police officer possesses (courpasson & montis, 2016; rubinstein, 1973) . moreover, there is the necessity to display 'tough and forceful' behaviors, represented by an aggressive, competitive, and performance-driven leadership style (silvestri, 2003 (silvestri, , 2007 . in so doing, machismo, an exaggerated version of masculinity, is a central element of police organizations. even for those who advocate a more nuanced view on masculinity in police organizations (see silvestri, 2017) , it is recognized that masculinity is a key element of police occupational culture, both amongst patrol officers (e.g. manning & van maaanen, 1978) and detectives (e.g. ericson, 1981; innes, 2003) . despite attempts to reform and make police organizations more gender-equal and less masculine, brown (2007) argues that machismo is a fundamental characteristic of police occupational culture and has become a core and basic assumption that informs the nature of police work and their work environment. if machismo and masculinity are cornerstones of police occupational culture, how will these elements play out in the extreme context of pandemic times when police officers need to be deployed to the front line? in this reflection, i will discuss this issue based on ethnographic research i have been doing with police detectives in brazil. in brazil, there are mainly two police forces at the state level: one responsible for patrol and crime prevention activities (the military police) and the other in charge of investigating crimes (the detective police). the research for this paper was conducted in the detective police force. brazil has one of the highest homicide rates in the world and uncountable public safety concerns. the police force also face several problems such as high rates of suicide and occupational diseases among detectives. much of equipment they use is obsolete and detectives this article is protected by copyright. all rights reserved. face severe difficulties in managing basic aspects of their work, such as logistics, managing people and financial resources. the research that inspires this paper adopts an ethnographic approach (spradley, 1980; van maanen, 1979; 2006; 2011) . despite the fact that this research has been on-going for almost 8 years and i have observed police activities in various police district areas (the homicide division, the anti-kidnapping division, the police academy and tactical units) for this paper i use data gathered during the first month of the covid-19 pandemic in brazil. i also teach pro bono regularly at the police academy, as a way to report back to the police on my findings and impressions from my research. i shall report a confessional tale that emphasizes fieldwork as a social construction (van maanen, 1988) . due to the long-term nature of this research, i developed a strong relationship of trust in the police force. today, i commonly receive phone calls from police personnel who reach out to me to tell stories. they are detectives with whom i would exchange daily smartphone instant messages and, before the pandemic, had lunch with or went out for a drink with at least once a week. the perception that the covid-19 pandemic was a real problem started as news arrived portraying the grave situation in italy, especially because many brazilians often travel to italy and on a regular basis. it was then that i started to wonder when the virus would arrive and spread in brazil and, as front-line workers, how the police would be severely impacted. i was very enthusiastic about doing fieldwork under pandemic times, as all over the world police forces are enacting containment measures and facing great the difficulties that this crisis poses. in brazil, officers have already been contaminated, and there is an ongoing need for the police worldwide to stay on the streets to either enforce lockdowns or even to collect samples for testing for covid-19. moreover, when the covid-19 pandemic arrived in brazil, i had just this article is protected by copyright. all rights reserved. moylan et al. 2015) . i am part of some police detectives' instant messaging groups and i can also easily reach police detectives via instant messaging and phone calls. each day, i have been writing very detailed field notes and memos (fretz et al., 1995) about the impact of covid-19 on police detectives. i follow an inductive research process that originates from my "thick description" of the field to generate an account that is both analytical and integrated into theory (van maanen, 1979) . i have also been inspired by spradley (1980: 14) who suggested "before you impose your theories on the people you study, find out how those people define the world". since my thoughts about being a researcher and not indiana jones and from the dialogues i was having with police detectives, it became this article is protected by copyright. all rights reserved. evident that the pandemic was challenging the heart of the police detectives to force masculine assumptions. i decided to write this because it helps me to deal with the social distance situation, my distancing from the ethnographic real-time fieldwork and as a way to think about the unprecedented challenges this pandemic situation will create for all of us. moreover, i think that doing police research has been linked to my masculine identity and having time to step back and be reflexive is always important. on march, 11th 2020 the world health organization (who) declared covid-19 a pandemic. two days later, i was meant to give a talk to 215 sworn-in police detectives at the management school where i work. this was part of a management module that i organize pro bono for the police detectives academy. given that the police force has severe mismanagement issues, i thought that bringing new detectives to be taught at this institution, one of the most renowned management schools in the country, would make a positive impression of the benefits of good management among the detectives starting their careers. this impression, i reckoned, would help them to remember the importance of good management for their institution in the years to come. on march 12 th , 2020 the head of my school decided to cancel all activities due to the fear of covid-19 spreading among our community and all our teaching activities migrated on-line. our school was one of the first educational institutions in brazil to cancel all classes. concerned about cancelling my talk altogether, the senior management at the police academy and i decided to give the talk at the police academy headquarters, even though the small auditorium would be crowded. two important cultural issues were at stake here. first, i learnt from police culture (maaning, 1977; rubinstein, 1973) that you have to keep your word to preserve your reputation. if you say you will do something, you had better do it. second, displays of fear are not taken well. saying that i would not teach due to personal concerns over this article is protected by copyright. all rights reserved. covid-19 would be seen as a "sissy behavior" and i would be the butt of little jokes. however, i knew if i cancelled the presentation, the police people would be completely fine about it. i was pressuring myself to do this. i felt that i had to keep my word even if this would mean i could be contaminated by covid-19. upon arriving in the academy to give my talk, i was informed that students were concerned about being in an overcrowded auditorium in times of covid-19. at the time, this seemed to be an overreaction. in mid-march, even though covid-19 was already a global threat, brazil was just two weeks into the aftermath of carnival, when millions of people took to the streets of the country to party and there were fewer than 20 covid-19 cases confirmed in the country. people were just starting to get worried about the virus, but life was going on as usual. when i was going to the lecture theatre, a police detective who works at the academy approached me and said, "professor, there are some students concerned about attending your talk due to covid-19. i don't understand, we are the police! if there is a zombie apocalypse, we are the ones who will need to get our weapons to hunt zombies down. how can they be afraid of a microscopic harmless creature for most of us? it is good this is happening; it is an opportunity for them to learn how to be a proper police detective earlier on". the idea here is that a "proper police detective" should not be afraid of any danger and also in face of danger needs to act. moreover, when i was discussing whether my talk and all other courses at the police academy should still go on, police detectives of the educational institution were telling me, "this is the police, not university. our mindset is different. they are not just studying, they are working. they are being paid to take classes. they need to be ready as soon as possible should we need extra manpower due to the pandemic situation. more importantly, we need to face the danger here, not run away from it". while giving my talk and facing an overcrowded room, i this article is protected by copyright. all rights reserved. start to ask myself what on earth i was doing there in pandemic times. being reflective of my practice, i began to realize that i was trying to show that i was also "brave", "strong" and "macho" in the eyes of the police detectives and myself. i realized that my need to display a hegemonic masculine identity had put myself in this risky situation. i apprehended how the police macho culture was stronger on me than i was aware of and this made me to completely realize how the police macho culture creates internal pressures for people to face risks. i also learnt that some detectives were complaining to the president of the detectives' union about the classes going on and also that non-urgent police activities were also going on. the union even requested legal help to force the police detective leadership to take action to protected detectives' health. on the same day this happened, some high-profile people from the military police contacted me saying, "this is totally absurd! we are the police and we need to be out there fighting crime. a warrior does not stop because of a virus". the masculine ideal of the warrior that does not fear the virus is explicit here. the military and the detective police engage in strong disputes, and this was taken as a way to suggest that the detective police is less engaged than the military. talking to a senior manager of the detective police, he said: "this legal request is embarrassing for us." the underlying idea here is that macho detectives should not be stopped by the virus. some of the detectives i spoke to from different police departments were starting to get worried about the total lack of occupational health and safety personal protective equipment (ppe) appropriate to protect detectives from being contaminated by the virus while working. the police mismanaged the purchase of ppe for some units and had to ask local businesses for donations of ppe supplies to the police. this is a common practice in brazil: police officers and chiefs ask a business to donate work equipment when none is available. antonio, one of the detectives complaining about the lack of ppe, is well-known for using his social media to show off pictures of him using heavy rifles and other symbols of hyper-masculinity. when this article is protected by copyright. all rights reserved. another detective told me about antonio, he mentioned "this is interesting. antonio shows off in his social media as if he was the top macho detective in the world. now, he is complaining that there is no ppe for him to work. come on! is he afraid now? what a sissy!" showing concern about covid-19 was being perceived as not appropriate for someone who likes to show off as the macho detective. even though the wearing of bulletproof jackets is obligatory for police detectives when using marked police cars, very rarely do they wear such protective gear. there is an underlying idea that using a bulletproof jacket is a display of being fearful and a "proper police detective" has no fear. the same was said by some concerning the use of ppe for covid-19, "i need no gloves or masks to work. i am a policeman". this was said at the very early stages of the pandemic in brazil. even a senior official of the police replied to a colleague when asked about the police plan for dealing with covid-19, "well, we finally guaranteed the necessary ppe for all police detectives. there is not a lot more we can do. everyone will be contaminated and we all will have to face the virus." the underlining idea is: the police job is to face danger". apart from ppe no other plan to protect the police force was being considered, most probably due to the prevailing mindset that police face danger anyway, so why would a plan be necessary? while covid-19 was not a strong reality in brazil, police detectives were working on a "business as usual" mode. under their macho police culture facing danger, making displays of hegemonic masculinity such as avoiding showing fear, was their reaction towards the virus threat. those who were showing fear or concerns over the virus were being challenged by their peers as if they were not macho enough to honor the police badge, they had. even my researcher self was feeling under pressure from the police culture to display masculinity, by teaching in an overcrowded auditorium. however, once the virus became a closer reality in the police, detectives started to change their behavior with regard to covid-19. this article is protected by copyright. all rights reserved. on march 19th, 2020 i was informed that 906 detectives were on sick leave with suspected covid-19. i could not confirm the veracity of those numbers, but some people i spoke to said, "there are a lot of contaminated police detectives". to make things worse, brazil did not have enough covid-19 tests and also the test results were taking more than 15 days to be released. as a detective told me "we are in the dark here. no one knows who is really infected. i don't know if the person who i work with is infected". it is rare to see a detective saying s/he does not know what is going on. they usually talk in such a way to show that they know what is happening. i was also informed that some students of the police academy had been admitted to hospital, even though they were less than 35 years old. i was later informed they had returned home safely. this led people from the police academy to comment that the virus was not as harmless as some were trying to picture it. as the presence of the virus became more pronounced in the detective police force, people started to get much more concerned. a senior detective told me, "i have never ever seen this in my entire career. for the first time ever, i feel people are afraid of what is going to happen. till now, our problems have been similar. we need to investigate and lock people up. that is what we know how to do best. now, we face an enemy we can't see, and we have never dealt with before. everyone who i know is afraid, i don't know what is going to happen". i heard this and similar comments from several people. also, some years ago, the police forces of the state were attacked by the drug gang that monopolizes crime in the region. many policemen were killed, but many more allegedly criminals were killed by police. compared to the times of the attacks, a detective said to me, "when we were under attack, it was much easier. to detain the virus. washing hands, using masks and gloves is not what they usually do when facing a threat. moreover, a detective talking to me said very worriedly "i am coming here to work every single day like everybody else on my team. do we all really need to come here every day? why they don't make some people come for 15 days and leave others at home. then, the ones who are home come to work. this could be a way to protect all of us". another police detective said "there are regulations that people over 60 should be working from home. however, my chief is ignoring this and is not sending anyone home. i have a friend who has just finished having chemotherapy and she is coming to work every day. how is that possible?". another detective contacted me to say, "i go in and out every day. i can get the virus and die or even kill my family". the tone of detectives talking to me has changed completely. they do not usually open show concern for their own or colleagues' safety. because of covid-19, they were all talking as if they were afraid of what would happen to them. when someone dies at home, the police have to investigate the death. the first response is usually made by the police district areas. once the police are informed that a person has died outside a hospital, a police squad goes to check the circumstances of the death. either the squad produces a formal report to say this was not a murder or they call the homicide department to start a murder investigation. it is only when this procedure has been followed that the corpse can be removed from the place where it is. with covid-19, the prospect of various deaths at homes made the police central management designate the homicide department in charge of checking all deaths. members of this department were fuming. one said to me "they are putting us and our families in real danger. why do we need to deal with this shit? we have no appropriate ppe, we have nothing. we will end up with this fucking virus." this particular detective never once wore a bulletproof jacket when i was following his squad on police operations and was terrified about coming into contact with the virus. this article is protected by copyright. all rights reserved. i also spoke to some detectives in the district areas. they were all very concerned about the virus and the means of protection against it. i have never once seen any detective complaining so harshly about the lack of ppe over my 8 years in the field. i spoke to a detective who said "in my district, there are not enough gloves and masks. also, we keep our door closed to stop people coming in. now, people can report crimes using the internet, there is no need to come to us. however, our general boss came to our station and told us off because the front door was closed. he says we need to keep working and he is making everyone turn up on the same day. if one gets the virus, we will all be contaminated". he also said, "the regional boss had a meeting in the station of one of my friends. the station boss had covid-19 and turned up to show off to the boss. can you believe? he was afraid of losing his chief position". moreover, a detective who assists a senior detective phoned me very worried saying "professor, people here are crazy. we have no serious plan to deal with this pandemic situation. how will we deal with the high amount of contaminated police detectives? how are we going to process all the bodies that will be in the city? how are we going to deal with organized crime in this pandemic situation? what is our plan to deal with domestic violence? i am exasperated! no one says anything. we are completely lost, no one knows what to do. this is a recipe for disaster". i asked if he had spoken to this boss. he replied "well, you know what they are like here. my boss thinks he is always right. he does not listen to anyone". the police have a very aggressive and non-collaborative management style. macho managers (panayiotou, 2010 ) are all around. the feelings of the police detectives on the ground are that the men at the top believe they know it all, as it is typical of macho leadership styles. in the pandemic situation, some chiefs are using a strong hand to make police to turn up to work while at the same time they do not feel protected to perform their tasks. the situation makes it even more explicit to police detectives how negative the aggressive management style they are under is. this article is protected by copyright. all rights reserved. when the death toll was approaching 1,000 deaths of covid-19 in brazil, a detective phoned me up to let me know about an argument he had had that day due to the behavior of one of his colleagues. he said "the person came into my office and wanted to shake hands. i asked if he was crazy and smiled. he got angry and said 'i am police, i shake the hands of my friends'. i replied that this was very dangerous. he replied that he was a policeman. i got very pissed off. come on! it is no time to shake hands!" he went on to complain about the behavior of his colleague. he also said that other people complained about that colleague, claiming he was mad. not shaking hands is a display of fear, and it was perceived by other police officer as the most appropriate reaction. the brazilian president, jair bolsonaro, has always used tough-on-crime and pro-police violence discourse. during the elections, he got massive support from police officers across the country. among the detectives i research, it was no different. the vast majority of police detectives who i spoke to had made positive comments about bolsonaro. far right populists exert hegemonic masculinity and machismo performances (knights & pullen, 2019) . this type of public personality embodies crucial elements of the police occupational culture. bolsonaro's son is a police officer. as the covid-19 situation evolved in brazil, bolsonaro tried to minimize the situation and was also against social distancing measures. he even said on a tv interview that "we need to take coronavirus like a man!". with his attitude of denial towards covid-19, bolsonaro started to lose respect and also popularity in brazil; a trend which has reverberated in the police. a detective who voted for bolsonaro said to me "this guy is crazy. he wants to kill all of us". also, a military police sergeant died of covid-19, the first police officer to die of the disease in the region where my research has been taking place. the news of this death rapidly spread in the police instant messaging groups with phrases like "many thanks bolsonaro, your reckless behavior will kill a lot of police officers in brazil". many detectives were saying that the president's attitudes were putting police officers' welfare at this article is protected by copyright. all rights reserved. risk. covid-19 was even challenging police's massive support of bolsonaro. this can be seen as a signal that in the pandemic situation the macho role model is undermined, even in an organization that is a prototype of the hegemonic masculinity organization. in this piece, i discuss the impacts of covid-19 on a prototypical hegemonic masculinity organization, the police. traditionally, a police force is an organization where the cult of masculinity is performed in everyday work (wilson, 1968; dick, 2005; o'neill, mars & singh, 2007; ) . the (macho) heroic police identity who fights crime (rubinstein, 1973; maaning, 1977; van maanen, 1980; bayley, 1994) is continuously performed through displays of virility, courage to face danger, toughness, showing interest in sexual triumphs, sports and outdoor life (van maanen & manning, 1978: 249) as well as the masculine favoring of reason over emotion (fassin, 2017) . machismo is a central element of police occupational culture up to the point of becoming a core and basic assumption informing the nature of police work, which can be very difficult to change. in the pandemic situation, at first, police were in the machismo "business as usual" mode. the core police machismo values of facing danger and avoiding displays of fear were initially the police reactions towards the virus threat. police detectives who were showing fear of the virus were criticized as if they were not "proper" police officers. i was even feeling this pressure in my interactions with police detectives and it took some time to decide that "i am not indiana jones", the adventure hunter, and that i should hold back my police research fieldwork. this shows how masculine values run deep and how this impact on people taking unnecessary and meaningless risks is just to display a type of masculinity. however, as the covid-19 situation in brazil worsened, police detectives started to feel the threat of the virus getting closer and closer. an important issue here is that often, police face dangerous criminals with weapons, ammunition and helicopters. however, all these key this article is protected by copyright. all rights reserved. artefacts in the police performance of police macho masculinity to fight the "war on crime" are totally useless to the police detective's engagement on the "war on the virus". to make matters worse, the virus is "confronted by" washing hands, wearing nurse-like masks and gloves and performing all different types of hygiene care. care is perceived in the police macho perspective as a non-macho masculinity attribute and wearing, even worst on the face, nurselike artefacts can be perceived almost as if you are non-macho. in addition, during the pandemic engagement with criminals should be avoided as much as possible. however, arresting criminals is how police officer display to each other how (macho) good they are. the covid-19 situation is not only making detectives to have to engage on culturally under valuated care-like activities, but it is also making the traditional police macho mindset redundant in the pandemic and causing an existential dilemma for policemen: to be protected against the virus, the police officer need to give away at least part of the embedded macho culture. the virus respects no occupational culture values. for many police officers, it is like if for protection against the virus, police officers cannot be who they have always been. in so doing, the virus ends up helping to undermine the traditional police macho culture because care does not resonate well in machism settings. police detectives have changed their "natural" macho behavior as they face this unknown situation. they indicated that they feared not knowing how to act in relation to the virus, and that they were concerned about the use of ppe, something very atypical. until the outbreak of covid-19, this was perceived as a display of fear and lack of masculinity. furthermore, subordinates were critical of stubborn macho leaders who did not listen and pretended to know it all. even hand shaking was being problematized and those who were trying to keep the same old macho habits were being criticized. the reaction against the president, a role model for machos in brazil, is also striking, as he was severely criticized even among his many of his supporters. the macho management style, either in the police or in the this article is protected by copyright. all rights reserved. country as a whole, was perceived as a "recipe for disaster" that would endanger the lives of the police officers. police detectives were shown to be frightened by the disease and displayed fear, something that is a no-no in macho organizations. either the pandemic situation seems to be putting police macho masculinity in danger (for the good), or at least it shows how problematic it can be for organizations. this piece indicates that the early stage of the pandemic is revealing how complicated machismo can be for organizations, especially during a pandemic, as it can literally put people's lives in danger. it also shows how an extreme situation can impact gender perceptions, performances and identities. however, as i finish this paper, the pandemic in brazil is still not as bad as in other countries such as the uk, the usa and italy, for example. however, the tendency is that the situation will get far much worse. this is a call for researchers to focus on how the pandemic can affect masculinity in particular and gender issues in organizations in general. the question we are left with is once this pandemic is over, will organizations go back to business as usual or will they be able to learn from this pandemic? back to the detective's police, the police academy has developed a training program to make police detectives offer a better and less judgmental approach to victims of domestic violence. the police macho culture has made detectives struggled to offer decent care for victims of domestic violence. this training involves role-playing in which the need to care for the other becomes clear. many police detectives seem to experiment a real change of behavior after taking part of the training program. the changing of a macho culture involves the need of people realizing the importance of care, both to the members of the organization and to the people they daily interact. police tend to see their jobs as "fighting-crime", however as the first respondents for crime victims, what police actually need to realize is that an important part of the police work is to care for people who just faced violence. covid-19 is making the need for care to be central in our can culture be managed? working with raw material: the case of the english slaughtermen confronting the digital: doing ethnography in modern organizational settings imagining gender research: violence, masculinity, and the shop floor. gender, work and organization what do the police do from cult of masculinity to smart macho: gender perspectives on police occupational culture coming out of the blue men and masculinities are not necessarily synonymous: thoughts on organizational behavior and occupational sociology naming men as men: implications for work, organization and management. gender work and organization breaking the silence: on men, masculinities and managements gender and power the big picture: masculinities in recent world history hegemonic masculinity: rethinking the concept i am my body'. physical selves of police officers in a changing institution understanding police culture dirty work designations: how police officers account for their use of coercive force to see ourselves as others see us? incorporating the constraining role of sociocultural practices in the theorization of micropolitical resistance. gender, work and organization the position of policewomen: a discourse analytic study what is hegemonic masculinity? theory & society this article is protected by copyright. all rights reserved making crime: a study of detective work enforcing order. ethnography of urban policing the organizational and occupational troubles of community police police cultures writing ethnographic fieldwork investigating murder: detectives work and the police response to criminal homicide note passing as gendered practices of public ambiguity in a hypermasculine organization. gender, work & organization managing masculinity in contemporary organizational life: a man(agerial) project. organization between representations and subjectivity: gender binaries and the politics of organizational transformation. gender, work and organization gender still at work: interrogating identity in discourses and practices of masculinity. gender, work and organization pushing the boundaries of amnesia and myopia: a critical review of the literature on identity in management and organization studies this article is protected by copyright. all rights reserved masculinity: a contested terrain? gender, work and organization managing masculinity/mismanaging the corporation. organization warriors in suits: a bourdieusian perspective on the construction and practice of military masculinity of korean men. gender, work and organization dominant culture interrupted: recognition, resentment and the politics of change in an english police force visible objects of concern: issues and challenges for workplace ethnographies in complex environments police work: the social organization of policing policing: a view from the street masculinities and crime: critique and reconceptualization of theory increasingly mobile: how new technologies can enhance qualitative research this article is protected by copyright. all rights reserved police occupational culture: new debates and directions macho' managers and organizational heroes: competing masculinities in popular films digital tools for qualitative research: disruptions and entanglements. qualitative inquiry doing hot and 'dirty' work: masculinities and occupational identity in firefighting. gender, work and organization little children are not for dad's?' challenging and undoing hegemonic masculinity. gender, work and organization there oughtta be a law against bitches: masculinity lessons in police training. gender work and organization editorial: undoing gender: organizing and disorganizing performance. gender, work and organization city police women in charge: policing, gender and leadership doing police leadership: enter the this article is protected by copyright. all rights reserved police culture and gender: revisiting the "cult of masculinity police and people of london. london: the policy studies institute the fact and fiction of organization ethnography career games: organizational rules of play tales of fieldwork: on writing ethnography ethnography then and now ethnography as work: some rules of engagement the killing consensus: police, organized crime, and the regulation of life and death in urban brazil varieties of police behaviour: the management of law and order in eight communities stress at work, gendered dysappearance and the broken body in policing. gender, work & organization an inside job: policing and police culture in britain this article is protected by copyright. all rights reserved.lives. macho public figures as bolsonaro who display contempt to the care of people are being severely questioned, even among ex-supporters. the hope is this deadly disease can, at last, teach the lesson of the need to care which will be a key element to challenge prevalent machismo in organizations and large parts of society. key: cord-342734-37xduboo authors: thomé, beatriz c.; matta, gustavo c.; rego, sérgio t. a. title: ethical considerations for restrictive and physical distancing measures in brazil during covid-19: facilitators and barriers date: 2020-11-09 journal: j bioeth inq doi: 10.1007/s11673-020-10023-w sha: doc_id: 342734 cord_uid: 37xduboo covid-19 was recognized as a pandemic on march 11, 2020. nine days later in brazil, community transmission was deemed ongoing, and following what was already being put in place in various affected countries, restrictive and physical distancing measures that varied in severity across the different states were adopted. adherence to restrictive and physical distancing measures depends on the general acceptance of public health measures as well as communities’ financial leverage. this article aims to explore and discuss ethical facilitators and barriers to the implementation of physical distancing measures within three dimensions: political, socio-economic, and scientific. furthermore, we would like to discuss ways to ethically promote restrictive and physical distancing measures in a large and unequal country like brazil. there is an urgent need for transparent, consistent, and inclusive communication with the public, respecting the most vulnerable populations and attempting to minimize the disproportionate burden on them. only a few months after the emergence of sars-cov-2, the pandemic was already exerting great pressure on countries' health systems. to slow down transmission and allow health systems some time to prepare for a surge in cases that would quickly overwhelm them, countries adopted prevention strategies. in march 2020, brazilian states started implementing physical isolation measures, which, in general, included school closures and suspension of commercial activities except for those related to food and health. movement was limited to essential activities. a month later, 60 per cent of the brazilian population was in physical isolation, with variability across the states (inloco 2020). in this paper we discuss ethical aspects of implementing physical distancing in brazil, as well as potential barriers and facilitators, in light of political, socio-economic, and scientific dimensions. adherence to public health measures largely relies on the public's trust in health systems. brazil's public health system, the sistema único de saúde or unified health system (sus), guarantees universal access to healthcare. primary care, routine immunization, and the hiv comprehensive care programmes are some of its success stories (castro et al. 2019) . research has shown that utilization of healthcare services, including for prevention, even if unequally across the regions, has increased overall in the past thirty years (viacava et al. 2018) . nevertheless, there has been a decline in the previously very high immunization coverage across the country (fujita et al. 2018) . austerity measures and underfunding of sus in the past years may help explain less vaccinepreventable diseases campaigns and the observed lower vaccination rates (fujita et al. 2018; massuda et al. 2018; paim 2018) . the resurgence of dengue in the country in the 1980s revealed the decreased efforts in improving sanitation in poorer settings, and the focus for dengue control has since been put largely on individuals and their ability to implement their own prevention methods, instead of placing the responsibility on governments to address underlying infrastructure problems (löwy 2017) . in the 2010s new viruses entered the country producing chikungunya outbreaks and also laying the grounds for the zika global health emergency in 2015-2016 (matta et al. 2019) . the arbovirus control strategy set the stage for the current covid-19 response in which the governments ask societies to play their part and stay home to tackle covid-19, without providing them with the necessary support. along with cuts in funding, the public's trust in the system may also have diminished, interfering with adherence to implemented public health measures to prevent covid-19 spread. in april, 54 per cent of brazilian adults interviewed thought physical distancing would not help contain the advancement of the pandemic (ipsos 2020) . we have witnessed a political polarization of covid-19 response and a lack of clear federal public health measures to tackle the pandemic, undermining the potential positive effects of a harmonized response. inconsistent prevention messages from government leaders, instability of health leadership at federal level, and lack of coordination of response across the administrative levels may have led to the public's distrust, thus affecting their response. furthermore, the failure of political coordination between federal and state governments is a critical moral issue and a source of misinformation. the moral face of the state institutional component, not only in brazil, is unfortunately immersed in misuse of political power and opportunism, at high costs for populations and the planet. adherence to prevention measures largely depends on social, cultural, and economic factors such as job security, housing, means of transportation, childcare options, and tensions between individual rights and collective protection, among others. crises such as pandemics will inevitably hit the most vulnerable harder. in particular, if people are deprived of their freedom of movement in a situation of physical isolation, those under no financial security will be most at risk for further impoverishment. this concern has been raised during the covid-19 pandemic (ahmed et al. 2020 ) and is of utmost relevance for brazil, where more than thirteen million people live in extreme poverty, defined as living below u.s. $2 per day (ibge 2019). recent estimates for brazil reveal an unemployment rate of 12 per cent, with over 40 per cent of the working population in informal employment (pnad/ibge 2020). this unemployment rate does not include the so-called disillusioned-that is, those who are available to work and would like to but have no expectation of finding work (ibge 2020). reasons why people give up looking for work include not finding work in the region, not finding adequate work, and not getting a job due to being considered too young or too old or because of no professional experience or qualifications. additionally, about 11.5 million brazilians live in houses with more than three people per bedroom (pnad/ibge 2020). the federal government has put in place social incentives to support families during the covid-19 crisis, with several limitations to access them. furthermore, these incentives had their implementation delayed and are planned to be paid for three months only, when financial constraints are expected to last for longer (folha de são paulo 2020). even among those eligible to receive the incentive, many have reported difficulties accessing the benefit. as a result, many people are lining up at the banks-in contravention of physical distancing guidance (g1 2020). as previously mentioned, the federal government started implementing economic constraints in 2019 based on an ultra-neoliberal agenda, radically reducing social protection investments like health, education, social security, science, and technology. there are critical ethical issues related to facing and responding to the socioeconomic repercussions of physical distancing in low-and middle-income countries (lmics) such as brazil. in a society embodying immense structural inequities, the scope and density of social and sanitarian justice could be the edge between life and death to the most vulnerable. large-scale physical distancing measures were put in place early in wuhan, at the start of the sars-cov-2 outbreak. at that point, little was known about the effectiveness of such measures, and ethical issues were raised concerning curbing people's right to move freely. months later, there is at least preliminary evidence that such measures have been successful in decreasing covid-19 transmission (prem et al. 2020; nussbaumer-streit et al. 2020) . to be ethically sound, the implementation of these physical distancing measures needs to be evidence-based, and evaluated and updated as we build collective knowledge on the pandemic (who 2020a). guidance from world health organization (who) highlights the role of testing for sars-cov-2 infection in the control of the pandemic. the response should be based on identifying and caring for covid-19 patients and quickly identifying their contacts, who can then monitor themselves for symptoms and self-isolate (who 2020b). in brazil there has not been a harmonized testing strategy, and testing overall has been very limited. at the end of april 2020, there had been 0.63 tests/1000 inhabitants, as compared to 12.0/ 1000 in the united states and 25.0/1000 in germany (bbc news brasil 2020). improving testing capacity, coupled with ensuring adequate care for covid-19 patients, would potentially facilitate the assessment of the pandemic impact in the various communities and redirect public health measures accordingly. finally, during a sanitary emergency, decisions need to be made according to scientific knowledge. the president, unfortunately, who does not express confidence in science, has made fighting the pandemic more challenging, as he has been acting against physical isolation guidance. measures to restrict the individual right to freely move are supported by an argument that collective interests should precede individual interests. this statement, however, is not equally accepted in different societies as well as in different historical contexts. discourse ethics (habermas 1990 ) provides an excellent framework for this analysis, as it assigns the task of defining what is right or wrong, what is just or unjust, to those who are affected by the norm. on this basis, the stringent standards that apply would be those that find acceptance by all those affected by it. in other words, the validity of the norm should not be conditioned by the interests of the most powerful or the most numerous but potentially by the interests of all. thus, we intend to defend a theory of ethics of mutual respect that would justify the possibility of accepting as correct, in principle, the hypothesis of establishing limitation of the individual right to freely move, as long as equal conditions are established for everyone affected by the norm. in principle, this condition is fulfilled when there is no exception for the physical distancing measures put in place based on who is affected. the difficulties in achieving physical distancing in the poorest brazilian communities reflect the conditions to which these population segments are subjected: overcrowded housing, inadequate sanitation, and little or no financial leverage. hence, to respect the ethics of reciprocity, we must offer conditions so that the most vulnerable receive additional resources to help them comply with such measures. considering that the social involvement of members of these communities is also desirable, it is necessary to listen to them and meet their needs. favelas (slums) have demonstrated excellent organization and action capacity during covid-19. however, governments rarely see their organizations as valid interlocutors, undermining communities' chances of having their voices heard. trust in health authorities and scientists has a major role in public acceptance of public health measures, as noted during the h1n1 pandemic by freimuth et al. (2013) . trust is established through relationships built over time and should not be merely expected based merely on government or public health institutions' exercise of authority (dawson et al. 2020) . trustworthiness is not established by decree. quite the opposite, trustworthiness develops when authorities' commitment, honesty, and concern are perceived by the public (freimuth et al. 2013) . o'neill has argued that rather than invest in increasing trust per se, we should aim at enhancing trustworthiness in our societies (o'neill 2002) . in particular during this sanitary emergency, when the trustworthiness of governments and public health agencies are the same time being challenged and heightened in relevance, we've witnessed authorities fail to achieve and stimulate the public's trust. unfortunately, sometimes, they are doing the opposite, spreading misinformation and distrust. each country will have its own challenges and social and cultural specificities when implementing public health measures to contain the covid-19 pandemic. we support an inclusive and equitable approach to public health measures that respects most vulnerable populations and attempts to minimize the disproportionate burden on them, as previously proposed (berger et al. 2020) . there is an ethical duty to protect the most vulnerable in particular during a pandemic. hence, understanding long-standing vulnerabilities (and how they are modified when facing the pandemic) as well as new ones generated by covid-19 will define how well we are able to protect them during physical distancing times. in particular, during an outbreak of this size, there is a need for transparent and inclusive communication with the public, which may require various strategies to reach different populations (who 2016). in brazil, open tv channels are the most used source of information on the pandemic, independent of social class (ipsos 2020) . communicating reliable information in dialogue with the public enables a true co-construction of understandings and practices-a pandemic narrative that produces public confidence and efficient responses to social and health needs and avoids misinformation and rumours. from a financial security perspective, who advocates for support to mitigate the financial and social impact of restriction of movement (who 2016) as part of an ethical response to infectious diseases outbreaks such as the one we're living with. although social support measures have been put in place in brazil, these need to be revisited and continuously adapted in light of people's real needs. all efforts should be put in place so that the population is well informed during the covid-19 pandemic and understands the reasons behind physical isolation along with other strategies and feels supported and included in the response. if such measures are accompanied by continuous public dialogue and participative evaluation that assesses both acceptability from the public as well as effectiveness, there is a higher chance the population will trust the health systems implementing them. trust in health systems is likely to produce a sense of social solidarity and a belief that we are in fact all fighting this pandemic together, despite different conditions and beliefs, and we will have a better chance to succeed. funding this work was partially supported by the wellcome trust -grant n. 218750/z/19/z. why inequality could spread covid-19 brasil é um dos países que menos realiza testes para covid-19 covid-19: control measures must be equitable and inclusive brazil's unified health system: the first 30 years and prospects for the future key ethical concepts and their application to covid-19 research. public health ethics: phaa017 demora nas ações de auxílio e invisibilidade de grupos agravam fome trust during the early stages of the 2009 h1n1 pandemic decreasing vaccine coverage rates lead to increased vulnerability to the importation of vaccine-preventable diseases in brazil com problemas para obter auxílio emergencial, trabalhadores geram filas nas agências da caixa no es moral consciousness and communicative action extrema pobreza atinge 13,5 milhões de pessoas e chega ao maior nível em 7 anos [extreme poverty reaches 13 2 0 2 0 . c o v i d -1 9 many think it's unlikely the economy will recover quickly once covid-19 lockdown is over. news leaking containers: success and failure in controlling the mosquito aedes aegypti in brazil zika outbreak in brazil: in times of political and scientific uncertainties, mosquitoes can be stronger than a country the brazilian health system at crossroads: progress, crisis and resilience quarantine alone or in combination with other public health measures to control covid-19: a rapid review a question of trust: the bbc reith lectures sistema único de saúde (sus) aos 30 anos the effect of control strategies to reduce social mixing on outcomes of the covid-19 epidemic in wuhan, china: a modelling study sus: oferta, acesso e utilização de serviços de saúde nos últimos 30 anos [sus: supply, access to and use of health services over the last 30 years managing ethical issues in infectious disease outbreaks considerations in adjusting public health and social measures in the context of covid-19 considerations in the investigation of cases and clusters of covid-19 key: cord-353996-slnyun4l authors: baumgartner, m. t.; lansac-toha, f. m.; coelho, m. t. p.; dobrovolski, r.; diniz-filho, j. a. f. title: social distancing and movement constraint as the most likely factors for covid-19 outbreak control in brazil date: 2020-05-08 journal: nan doi: 10.1101/2020.05.02.20088013 sha: doc_id: 353996 cord_uid: slnyun4l as thousands of new cases of covid-19 have been confirmed, there is an increasing demand to understand the factors underlying the spread of this disease. using country-level data, we modeled the early growth in the number of cases for over 480 cities in all brazilian states. as the main findings, we found that the percentage of people respecting social distancing protocols was the main explanatory factor for the observed growth rate of covid-19. those cities that presented the highest spread of the new coronavirus were also those that had lower averages of social distancing. we also underline that total population of cities and connectivity, represented by the city-level importance to the air transportation of people across the country, plays important roles in the dissemination of sars-cov-2. climate and socioeconomic predictors had little contribution to the big-picture scenario. our results show that different states had high variability in their growth rates, mostly due to quite different public health strategies to retain the outbreak of covid-19. in spite of all limitations of such a large-scale approach, our results underline that climatic conditions are likely weak limiting factors for the spread of the new coronavirus, and the circulation of people in the cityand country-level are the most responsible factors for the early outbreak of covid-19 in brazil. moreover, we reinforce that social distancing protocols are fundamental to avoid critical scenarios and the collapse of healthcare systems. we also predict that economic-induced decisions for relaxing social distancing might have catastrophic consequences, especially in large cities. in late december, 2019, the novel coronavirus disease 2019 emerged in wuhan, the capital city of hubei province in great china . at the beginning of the infection outbreak, the disease caused by the sars-cov-2 virus has been suggested to be of bat origin (cheng et al., 2007; guo et al., 2020; zhou et al., 2020) , and might have been transmitted to humans through intermediate mammals (andersen et al., 2020; zhang et al., 2020) . the initial diffusion of the virus suddenly became exponential, increasing the number of infected cases and deaths in wuhan . in the next few weeks, it has become clear that the high virulence of the new coronavirus posed a considerable health threat on a global scale, quickly spreading to asia, europe, north america, and, more recently, south america and africa. on march 11, 2020, the world health organization (who) declared the coronavirus as a global pandemic. the declaration reflected the concern by who that countries were unable to control the dissemination of the virus . the novel coronavirus is still spreading rapidly worldwide, with millions of infections and hundreds of thousands deaths addressed to covid-19, most of them concentrated in the united states and europe. common symptoms of covid-19 infections include fever, dry cough, and dyspnea but the most serious clinical case is lung failure associated with severe acute respiratory syndrome (sars) . from all infected patients, about 30% require mechanical ventilation and 2-5% die, with higher death rates in elderly people and those with comorbidities (rothan and byrareddy, 2020) . fortunately, most people have very mild symptoms or are even asymptomatic . conventionally, laboratory testing by real-time polymerase chain reaction (rt-pcr) and quick antigen tests have been conducted prioritizing symptomatic or high-risk groups (mizumoto et al., 2020) . however, a recent study showed that substantial undocumented infection facilitates the rapid dissemination of the novel coronavirus (r. , which forced the who to recommend that policymakers should mobilize mass testing in an attempt to retain initial local outbreaks effectively (balilla, 2020) . with clinical symptoms that are indicative of many ordinary conditions, the new coronavirus is the largest concern for human populations because it may cause severe clinical conditions that can readily overcome the carrying capacity of healthcare facilities. although vaccines and immunotherapy protocols have been conducted in a rate never seen before, there is no effective treatment for covid-19 yet (lurie et al., 2020) . the available interventions include rapid diagnosis and isolation of confirmed cases, and restrictions on mobility . especially for in-development countries, social isolation has been listed as the most effective strategy to deal with covid-19 and mitigate the risk for public health and economy (coelho et al., 2020) . however, understanding how other environmental and social factors are associated with human-to-human transmissions of sars-cov-2 are fundamental for the decisionmaking process at a country-level. building on evidence about the role of environmental factors such as temperature and humidity on the survival of viruses, some studies forecasted the near future of the current outbreak (sajadi et al., 2020; wang et al., 2020) . for instance, araújo and naimi (2020) built a global ensemble to model the monthly spread of covid-19 under the prediction of temperature and humidity, although with some later criticism (chipperfield, 2020) . while these variables are known to interfere with the spread and survival of other coronaviruses (e.g., sars-cov and mers-cov; gaunt et . 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 8, 2020 . . https://doi.org/10.1101 .05.02.20088013 doi: medrxiv preprint al., 2010 chan et al., 2011; cauchemez et al., 2014) , considering only the environment and ignoring social and behavioral factors might be inadequate to determine effective restraint strategies in the near future (pybus et al., 2015) . considering socioeconomic aspects, countries and regions across the world have a very skewed distribution of income and wealth (dabla-norris et al., 2015; davies et al., 2017) . even within countries, there are clear spatial distribution patterns of economic development, as it is explicit within brazil (skidmore, 2004) . in terms of healthcare, socioeconomic indicators can be considered as a proxy for the ability of each city to identify and treat people with covid-19 effectively (coelho et al., 2020) . additionally, the dispersal of viruses among hosts follows a geographic pattern (holmes, 2004) . thus, the physical distance among cities (and people) is certainly crucial for how the actual pandemic state will evolve (chipperfield, 2020) . in an attempt to investigate these factors, coelho et al. (2020) found evidence that the air transportation of people across the word overcame environmental and socioeconomic factors, posing a strong argument towards social distancing and traveling restraint. thus, here we extended the investigation on which factors could be related to the spread of the new coronavirus in brazil, considering all cities on a nation-wide scale. we studied the exponential growth of time series data for over 460 cities with reported cases of infections by the new coronavirus, considering the effect of the environment, socioeconomic indicators, movement of people across the country, and social distancing. we demonstrate that the growth of covid-19 in different cities is mostly determined by population size, transportation among cities, and the percentage of people respecting social distancing protocols. this evidence points towards social distancing and mobility restriction as the main actions necessary to reduce the spreading of the pandemic and avoid its worst consequences. we obtained data on the daily number of people manifesting the covid-19 in brazil, available at the digital panel from the ministry of health (http://www.covid.saude.gov.br). this dataset comprises real-time information on disease cases that were confirmed through laboratory analysis and quick tests for every city. our most recent data retrieval was conducted on april 20, 2020, which comprised information of 40,581 cases and time series data for 1,456 cities with at least one confirmed case, since the first recorded case in brazil on february, 25, 2020. we chose april 20 as the last day because several cities have gradually relaxed their quarantine protocols and allowed many working activities to restore their functioning since then. in our analyses, we used only the exponential part of each time series by excluding previous days before the first confirmed cases in each city, and no time series had reached stabilization or decrease in the total number of confirmed records yet. we fitted exponential growth models to the time series of each city and calculated the intrinsic growth rate (r), as well as the slope coefficient (b) of the loggrowth model. because our focus was on the overall growth of the number of confirmed cases, these two parameters were candidates to be used as response variables in our approach. however, some convergence failures for exponential models applied on short time series and the high goodness-of-fit of log-transformed models (average r² = 0.84) led us to use the log-growth slope in our subsequent analysis. in order to explore potential correlates of the early increase in the number of cases, we used climatic and socioeconomic data. climatic variables included average . 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 8, 2020. . temperature (ºc) and precipitation (mm), retrieved from the most recent year available at the worldclim online database (http://www.worldclim.org; fick & hijmans, 2017) . this database comprises monthly information on these climatic variables. we downloaded temperature and precipitation values between february and april, which coincided with the time series of covid-19 cases in brazil and with the late summer season of the southern hemisphere, matching the world outbreak of the virus. from these data, we extracted values for each city according to their geographic coordinates, using the qgis 3.12.1 software (qgis development team, 2020). for each city, we also extracted information on total population, human as an additional correlate to the increase of the infestation by the new virus, we also considered information on transportation of people across the country. first, we obtained data on air transportation available at the openflights database (http://openflights.org/data.html), which included information on 122 airports within brazil, and whether there is a direct flight connecting each pair of them (1,193 flights). to match the information on the spread of the virus across cities, we filtered these airport records to consider only those cities that had at least one confirmed infection, which yielded us a database containing 100 cities with 1,164 registered flights (fig 1) . we then used these cities and flights to construct an oriented graph with cities assigned as notes and flight routes as edges (west, 2001) . from this network, we extracted a . 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) variable that weighted the importance of each city to the country-level network: the eigenvector centrality (bonacich, 1987) . this metric quantifies both how surrounding cities are connected to a focal city and its connection to the whole network, directly and indirectly. second, many cities with confirmed cases are not large enough to carry airports with commercial flights. in these cases, we used the geographic coordinates to calculate the proximity to the nearest airport (1 -standardized euclidean distances), which was then multiplied by the centrality of their respective nearest airport. these two procedures yielded connectivity, a variable that represented the direct and indirect movement of people among large cities, based on their centrality, as well as their potential exchange of people with smaller municipalities nearby, described by the proximity-weighted centrality. brazil by april 20, 2020. blue circles represent cities with less than five confirmed cases, which were not included in our analyses. yellow, orange, and red symbols depict cities that had at least five confirmed cases, with (82 cities; triangles) and without (383 cities; circles) airports. flying routes are depicted by gray traces and state borders are in black. see fig. s1 for more details on the names and locations of each brazilian state. . 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 8, 2020. . in order to assess the effectiveness of social distancing on the early spread of the new coronavirus in brazilian cities, we used state-level data on mobility of citizens (https://mapabrasileirodacovid.inloco.com.br/), which comes from a monitoring program that was exclusively implemented to be useful against the new coronavirus. this database comprises the percentage of people performing social distancing for each state on a daily basis. the index is based on information provided by telephone companies about the location of electronic devices (e.g., cellphones and tablets), which are tracked through their physical displacement under wi-fi, bluetooth, and gps connections. in practice, whenever an electronic device leaves a radius of ~200 m from what it is considered as 'home', the system records the event as a movement. therefore, this protocol ensures the privacy and preserves the identity of citizens by focusing on the binary record of movement, rather than on the destination or specific routes of each citizen. this information yielded us a database with the time series of social distancing for each state. to obtain city-level data, we averaged the percentages between the first day of covid-19 record in brazil and the day where the thresholds of the minimum number of cases was achieved at each city (see below). see supplementary material we investigated whether the city-level growth rate of covid-19 was related to the climatic, socioeconomic, connectivity, and social distancing predictors using multiple linear regression models. models were fitted using sequential subsets of the 465 cities considering increasing thresholds of the minimum number of confirmed . 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 8, 2020. . cases: 5, 10, 20, 40, 80, and 160. this sequential sub-modelling approach intended to assess whether and how the covid-19 outbreak across brazil was related to each one of our predictors along the early spread of the disease, considering cities at different stages of the dissemination wave. all predictors were checked and only total population required log transformation to approximate a normal distribution. before statistical analyses, we checked the multicollinearity of predictors, by computing the variance inflation factors (vif), and removed those that the variance of a regression coefficient was inflated in the presence of other explanatory variables (i.e. vif > 5; (borcard et al., 2018) ). in this case, hdi and average income showed collinearity, so we kept the later in our analyses because of its larger variation. in addition, we used moran's i correlograms (legendre and legendre, 2012) to check if the control for spatial autocorrelation bias was required, which could somehow inflate the significance of each predictor. a summary of all the predictors used to fit the regression models is provided in fig 2. finally, we fitted independent linear models to each state to investigate potential regional trends in the covid-19 growth, using the most important predictors identified in the previous steps, separately. for this procedure, we used only those states that had at least five cities with at least five confirmed cases. for inference, we then plotted the log-transformed total number of confirmed cases against the standardized slopes of the models, which portrays the state-dependent context of growth in covid-19 cases. all analyses were performed in the r environment (r core team, 2019) using packages ape (paradis and schliep, 2019) , car (fox and weisberg., 2019) , and igraph (csardi and nepusz, 2006) . . 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 8, 2020. . brazilian maps showing the geographic patterns of all predictors considered in the regression models: temperature (a), precipitation (b), log-total population (c), average income (d), connectivity (e), and social distancing (f). states borders are depicted by black traces and colors of each state represents the mean value considering all cities. circles depict cities that had at least five confirmed cases. the colors within circles represent the values of each predictor, whereas the circle size depicts the b log growth rate (logb) for each city. . 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 8, 2020. . https://doi.org/10.1101/2020.05.02.20088013 doi: medrxiv preprint the overall performance of models fitted to the exponential growth of covid-19 in each city was particularly good. the average variance explained by our predictors (r²) were 0.51 (>= 5 cases; 465 cities), 0.60 (>= 10 cases; 252 cities), 0.61 (>= 20 cases; 158 cities), 0.64 (>= 40 cases; 104 cities), 0.56 (>= 80 cases; 62 cities), and 0.67 (>= 160 cases; 33 cities). considering the effect of each predictor on the exponential growth across all sub-models, social distancing had significant relationships in all cases, with an average standardized coefficient of -0.15 (table 1, fig 3) . this variable was also the only with negative significant slope coefficients. most importantly, social distancing had an intensifying trend in its negative coefficient across sub-models, showing an enhanced effect as the number of confirmed cases evolved. in addition, total population and connectivity of each city had significant relationships in five out of six sub-models, with average standardized coefficients of 0.14 and 0.07, respectively. another predictor that played a secondary role was precipitation, which was significant in the first four sub-models, although with a considerably weak average standardized coefficients (0.05). average income was only significant for the first sub-model, whereas temperature was not significant in any sub-model. none of the six sub-models presented bias related to spatial autocorrelation structures according to moran's i correlograms. . 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 8, 2020. . fig. 3 : relationships between the slopes of log-growth models fitted to time series of confirmed covid-19 cases for every city. only significant regression models are shown. comparatively, the variable with the clearest effect on the exponential growth during the covid-19 early outbreak was social distancing (table 1; fig 3e) . in practice, this result suggest that the more frequent people circulated within cities (lower . 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 8, 2020. . https://doi.org/10.1101/2020.05.02.20088013 doi: medrxiv preprint social distancing), the faster the early spread of the new coronavirus (a result that was consistent across all sub-models). the results also reveal that the log-growth of the disease caused by the sars-cov-2 virus increased with the total population of cities (fig 3) . thus, larger population sizes led to faster spread of the new coronavirus. the third most important variable, connectivity (fig 3d) , had a similar trend but with considerably lower standardized coefficients (at least two times lower than total population, table 1 ). in contrast, we observed that precipitation (fig 3a) showed trends that were more important during the initial days in each city, with positive but very low coefficients (table 1) . when we built one independent model for each state, considering total population, connectivity, and social distancing (i.e., the three most important predictors), there was a high variation in the results depending on the focal state (fig 4) . notably, the rate of increase in the number of covid-19 cases was mostly determined by respecting social distancing protocols (i.e., higher r²; fig 4c) , followed by population size (fig 4a) . although not with the same intensity, connectivity also had an important role on the observed growth patterns (figure 4b ). . 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 8, 2020. . https://doi.org/10.1101/2020.05.02.20088013 doi: medrxiv preprint the overall trend was that those states where people were performing social distancing less effectively (leftward circles in fig 4c) in addition to the pandemic state and the thousands of deaths caused by covid-19 worldwide, some government boards and leaders manifest that their foremost concern regards the economic retraction, which is expected to last longer than the harmful effects of the covid-19 outbreak themselves. in fact, they are not completely controversial from their perspective. while in-development countries' systems depend on economic income (e.g., sales of commodities), further projections are certainly contingent upon the creation and offer of jobs to remain sustainable. however, the . 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 8, 2020 . . https://doi.org/10.1101 transmission of the virus and the complications arising from severe illness conditions may never rest on the bottom of the country-level priorities of one's management actions. by contrast, decision-makers should provide raw information to fuel research and development of effective containment and treatment of diseases. hereafter we discuss our results in light of the situations that other countries and cities around the world have experienced. our results show that the early spread of the new coronavirus in brazil was mitigated by social distancing in some regions, but was also positively related to the size of the population of cities and how people moved across them. these outcomes underline that the direct and indirect contact among individuals was the most responsible for the rapid spread of the disease caused by the sars-cov-2 virus in brazil. contrary to initial perspectives, the ability of covid-19 to spread, estimated by the basic reproduction number (r0) statistic, seems to be higher than the who estimated . moreover, substantial transmission before symptom onset facilitates the rapid dissemination of the novel coronavirus (hellewell et al., 2020) . as diseases transmitted by respiratory droplets require a certain proximity of people, social distancing certainly reduce transmission rates (anderson et al., 2020) . for this reason, keeping people apart from each other, whenever feasible, should be the primary goal of public health programs to prevent human-to-human transmission. we found evidences that the tools adopted by states and municipalities, including the closure of schools and commercial buildings, lock down of restaurants and malls, and prohibitions of mass gatherings had a negative impact on the expansion of covid-19 in brazil. most importantly, this result somehow evidences that the combination of ignoring social distance especially in large and well connected cities will have catastrophic consequences. . 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 8, 2020 . . https://doi.org/10.1101 in great china, the ongoing covid-19 outbreak expanded fast throughout the country and the majority of early cases reported outside of its origin had admitted recent travels to wuhan, the core of the disease spread (chinazzi et al., 2020) . because of the association between both international and domestic air travel and the dissemination of covid-19 (bogoch et al., 2020; zhao et al., 2020) , one of the initial plans for the contagious control was to prevent people from flying around when the outbreak emerged . actions such as reducing human mobility by restricting travels and declaring quarantine were fundamental to reduce the dissemination of sars-cov-2 within and outside wuhan, highlighting the importance of mobility restrictions in cities where there is a clear potential for spread of the new coronavirus (fang et al., 2020) . fortunately, in china, the government-level positions were declared when contagious boundaries were relatively discrete . comparatively, this was not the case in brazil, where the number of confirmed cases of covid-19 are still growing exponentially (crokidakis, 2020) . the first case in brazil was registered on february 25, 2020, in são paulo city (rodriguez-morales et al., 2020). it was a man with recent travel to the italy, precisely for the lombardy region. contrary to china, italy did not conduct a fast protocol of social isolation and already had a high number of cases and deaths. similarly to the observed in the united states, until the establishment of local transmission in brazil, all reported cases had returned from recent travels abroad. among them, it is noteworthy that 23 members of the delegation that accompanied the brazilian president on a visit to the united states in march had since tested positive for covid-19. indeed, the proportion of estimated imported cases by airport of destination is highly correlated with the proportion of detected imported cases (candido et al., 2020) . for this reason, the brazilian government announced a temporary ban on foreign air travelers by march 31, 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 8, 2020. . https://doi.org/10. 1101 moreover, most state governors have imposed quarantines to contain the spread of the virus, but with no support from the federal government. a recent study suggests that more than 40% of social isolation in brazil is necessary to flatten the epidemic curve of the new coronavirus and to prevent the collapse of the healthcare system . we defend that the only feasible way to achieve this target is to keep on with social distancing and avoid gatherings of people. despite the aforementioned efforts, most of them being contemporaneous among many countries, the effective containment of covid-19 is still a delicate task because of the characteristic mild symptoms and the transmission before the full onset of the disease (fraser et al., 2004; . however, the example of the sanitary action conducted in great china was fundamental when the contagious boundaries were discrete. in brazil's context, there are cities such as são paulo, rio de janeiro, and other capitals such as fortaleza and manaus that likely act as superspreaders of sars-cov-2. in a network context, these cities maximize their influence on covid-19 spread by exporting many cases to cities nearby (madotto and liu, 2016) . this fact highlights that these centers should be of foremost concern, especially because some of them are near (e.g. ceará and rio de janeiro) or have already saturated (e.g., manaus) their health system carrying capacity, given that the number of cases is growing very fast (crokidakis, 2020) . therefore, the multiple potential wuhan-alike regions in brazil require government-level actions towards the necessity of multiplicative movement restrictions and social distancing. moreover, there are speculations that the number of documented brazilian cases is likely more than ten times lower than the real number (bastos and cajueiro, 2020) , considering that tests are being conducted mostly only in cases of severe acute respiratory syndrome (sars). as an alternative to contour this situation, especially in those countries where several . 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 8, 2020. . undocumented cases are expected (e.g., in brazil), decision-makers could base their actions on the recent increase in number of sars-related hospital records as a surrogate to the real amount of covid-19 cases. in addition to social distancing and restrictions on mobility, interventions available include rapid diagnosis and isolation of confirmed cases . however, in brazil, the diagnosis is completely biased towards people already at advanced clinical stages, in contrast to other countries such as china, singapore, germany, and the united states. clearly, the growth rates of infections by the new coronavirus differ across countries (coelho et al., 2020; ficetola and rubolini, 2020) . as the rate differs, the factors determining the expansion of the infection within populations inevitably result from the policies adopted by each country. our results reveal that this variation also occurs within brazil. we believe that the reasons for this can be addressed to the continental-wide nature of our country, or the non-uniform demographic distribution across regions (reis-santos et al., 2013) . thus, the responsibility for the local spread of covid-19 is directly dependent on mayors' and governors' positions. several studies have shown that environmental factors such as local temperature and precipitation may affect the sars-cov-2 virus survival and transmission, with significant consequences for the seasonal and geographic patterns of outbreaks (bukhari and jameel, 2020; ficetola and rubolini, 2020; ma et al., 2020) . the mechanism underlying these patterns of climate determination is likely linked with the ability of the virus to survive external environmental conditions prior to reaching a host (harmooshi et al., n.d.) . a recent study showed that covid-19 is more viable at lower temperatures (5-11°c) and was inversely related to humidity (sajadi et al., 2020) . however, our results indicate that climate variables had secondary roles in explaining the covid-19 . 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 8, 2020. . growth rate in brazil. this weak relationship suggests that seasonal climatic variation plays a minor role in the spatial spread and severity of covid-19 outbreaks, as observed in recent studies on other regions (baker et al., 2020; coelho et al., 2020) . for instance, manaus, the largest metropolitan city in north brazil, is located at the core world's largest rainforest, the amazon, and is characterized by extremely high rainfall and temperatures throughout all over the year. this city registered more than one thousand confirmed cases and, recently, the state health department is suffering from the collapse of the health network due to the excessive cases of covid-19. among these, over 85 cases have been recorded in indigenous peoples and four deaths have been confirmed, including young people. historically, due to the absence of antibodies, indigenous people are likely more susceptible to diseases such as flu, measles, rubella, and tuberculosis, which caused dramatic epidemic cases with the arrival of europeans on the south american continent (montenegro and stephens, 2006) . according to the latest census, more than 300 thousand of indigenous people currently live in the amazon region, which is home to more than 100 tribes that are still isolated. the advance of illegal mining is a major threat to these peoples. furthermore, instead of allowing religious missionaries to get in contact with isolated indigenous groups, all means of transportation to these areas should be restricted (ferrante and fearnside, 2020) . therefore, the thoughtlessness by the federal government about covid-19 potentially leads to a dramatic scenario for indigenous people. it is important to highlight that the low predictability of climatic variables in explaining the virus outbreaks patterns may be explained by the climatic peculiarities of brazil during the summer that matched with the arrival and spread of the virus. among all cities with confirmed cases, the average temperature was 24°c and the lowest temperature was 18°c, which is still far from what was indicated as ideal for the . 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 8, 2020. . https://doi.org/10. 1101 survival of the virus (sajadi et al., 2020; wang et al., 2020) . we found a positive relationship between temperature and precipitation variables and the growth in the number of covid-19 cases, which is in line with previous findings in brazil (auler et al., 2020) , but contrary to a global tendency. although the coefficients were quite weak, this suggests that high temperatures and precipitation are not limiting factors for the spread of the virus. conversely, a scenario of extreme concern is emerging, since the winter season approaches, so temperatures will drop dramatically across many areas, especially in the south region. therefore, at this early outbreak, any generalization is hasty and results have to be considered with extreme caution. most importantly, the climate must not be used as an easing argument as particularly declared by the brazilian president. the actual emergence of the novel infectious agent has revealed the vulnerability of societies to new health threats (morse et al., 2012) . brazil has recently experienced other public health emergencies under polio, smallpox, cholera, h1n1 (influenza a), avian flu, yellow fever, dengue and zika . along with the current covid-19 outbreak, we judge that all these examples constitute an important legacy on the role of scientific research on dealing with epidemics. thus, we may now face the most important event, in the recent decades, to learn on how to respond to emergencies effectively . we need to assume that this study does not intend to serve as specific guidelines for any decision-making process within any specific administrative council. nevertheless, at a country-scale, we disapprove any government declaration or exposure that confronts the statements and protocols from the world health organization (who) or the united nations (un), which are international institutions that are presumed to be sovereign in their actions and recommendations since their utmost concern is the health . 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 8, 2020 . . https://doi.org/10.1101 and human wellbeing on a global scale. if eventually confronted, the arguments for doing so should be based on clear and strong scientific evidence, although it is very unlikely that these organizations have ignored such information while developing their protocols. it is now clear that the most likely determinant of the virus spread is the vicinity of infected peoples and cities. while evacuating cities is not reasonable at this point, the easiest and the most feasible way to decelerate the covid-19 spread is to avoid people transportation among them. this is fundamental within cities. while the virulence of the sars-cov-2 virus is remarkably high and we are not able to tear houses or buildings apart, the only way to allow for the healthcare systems to treat ill people effectively is performing social distancing. in the absence of any effective treatment and vaccine, we support that social distancing is still the only feasible way to avoid the collapse of our national health system. specially in brazil, a '3rd world country', we have few hospitals and clinics with beds and respirators that are autonomous for treating sars, which means that if we allow it to grow fast by not maintaining restrictions in movement between cities/states and social distancing within cities, we may certainly hope for the best but expect for the worst. we assume that the indicator for the efficiency of social distancing is a conundrum because the response about its effectiveness might come only weeks after the execution of any plans. in fact, people tend to underrate social isolation because the more effective it is, the less needed it seems to be. we also admit that any delayed action can be catastrophic, both for the health and economy of any country. nevertheless, the expeditious suspension of social distancing under the coating of restoring the economic trades and jobs likely has even more dangerous side effects than covid-19 itself. . 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 8, 2020 . . https://doi.org/10.1101 the proximal origin of sars-cov-2 how will country-based mitigation measures influence the course of the covid-19 epidemic? spread of sars-cov-2 coronavirus likely to be constrained by climate evidence that high temperatures and intermediate relative humidity might favor the spread of covid-19 in tropical climate: a case study for the most affected brazilian cities susceptible supply limits the role of climate in the covid-19 pandemic assessment of covid-19 mass testing: the case of south korea modeling and forecasting the early evolution of the covid-19 pandemic in brazil pneumonia of unknown aetiology in wuhan, china: potential for international spread via commercial air travel power and centrality: a family of measures numerical ecology with r will coronavirus pandemic diminish by summer? ssrn electron routes for covid-19 importation in brazil middle east respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility the effects of temperature and relative humidity on the viability of the sars coronavirus severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection the effect of travel restrictions on the spread of the 2019 novel coronavirus (covid-19) outbreak. science (80-. ). 9757, eaba9757 on the inadequacy of species distribution models for modelling the spread of sars-cov-2 : response to araújo and naimi. medrxiv exponential phase of covid19 expansion is not driven by climate at global scale covid-19 in brazil: advantages of a socialized unified health system and preparation to contain cases data analysis and modeling of the evolution of covid-19 in brazil the igraph software package for complex network research causes and consequences of income inequality: a global perspective estimating the level and distribution of global wealth human mobility restrictions and the spread of the novel coronavirus (2019-ncov) in china protect indigenous peoples from covid-19 climate affects global patterns of covid-19 early outbreak dynamics worldclim 2: new 1-km spatial resolution climate surfaces for global land areas an r companion to applied regression factors that make an infectious disease outbreak controllable epidemiology and clinical presentations of the four human coronaviruses 229e, hku1, nl63, and oc43 detected over 3 years using a novel multiplex real-time pcr method the origin environmental concern regarding the effect of humidity and temperature on sars-cov-2 ( covid-19 ) survival : fact or fiction 2 feasibility of controlling covid-19 outbreaks by isolation of cases and contacts the phylogeography of human viruses the effect of human mobility and control measures on the covid-19 epidemic in china numerical ecology substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov2). science (80-. ). 3221, eabb3221 evolutionary history, potential intermediate animal host, and cross-species analyses of sars-cov-2 the reproductive number of covid-19 is higher compared to sars coronavirus developing covid-19 vaccines at pandemic speed effects of temperature variation and humidity on the death of covid-19 in wuhan super-spreader identification using estimating the asymptomatic proportion of coronavirus disease 2019 (covid-19) cases on board the diamond princess cruise ship indigenous health in latin america and the caribbean ape 5.0: an environment for modern phylogenetics and evolutionary analyses in r virus evolution and transmission in an ever more connected world qgis development team, 2020. qgis geographic information system r: a language and environment for statistical computing socio-demographic and clinical differences in subjects with tuberculosis with and without diabetes mellitus in brazil -a multivariate analysis the implications of the first confirmed case in brazil the epidemiology and pathogenesis of coronavirus disease (covid-19) outbreak temperature and latitude analysis to predict potential spread and seasonality for covid-19. ssrn electron policy issues brazil's persistent income inequality: lessons from history high temperature and high humidity reduce the transmission of covid-19. ssrn electron introduction to graph theory prevalence of comorbidities in the novel wuhan coronavirus (covid-19) infection: a systematic review and meta-analysis probable pangolin origin of sars-cov-2 associated with the covid-19 outbreak quantifying the association between domestic travel and the exportation of novel coronavirus (2019-ncov) cases from wuhan, china in 2020: a correlational analysis a pneumonia outbreak associated with a new coronavirus of probable bat origin a novel coronavirus from patients with pneumonia in china this study was developed as a contribution to the brazilian ministry of health about the overall evaluation of collected data on covid-19. most of the merit of this study belongs to all those individuals involved in collecting epidemiologic data and working in favor of health, directly or indirectly, inside or outside the healthcare facilities. they deserve sincere acknowledgements for their daily work. mtb conceived the study with extensive suggestions from fmlt. mtb gathered and organized information and fmlt analyzed data. visual results were produced by fmlt. mtb and fmlt wrote the first draft, which was thoroughly reviewed and approved by all authors. key: cord-329401-b09wj0h7 authors: fernandes, m.c.; takai, s.; leite, d.s.; pinto, j.p.a.n.; brandão, p.e.; santarém, v.a.; listoni, f.j.p.; da silva, a.v.; ribeiro, m.g. title: identification of pathogens and virulence profile of rhodococcus equi and escherichia coli strains obtained from sand of parks date: 2013-10-30 journal: braz j microbiol doi: 10.1590/s1517-83822013005000044 sha: doc_id: 329401 cord_uid: b09wj0h7 the identification of pathogens of viral (rotavirus, coronavirus), parasitic (toxocara spp.) and bacterial (escherichia coli, salmonella spp., rhodococcus equi) origin shed in feces, and the virulence profile of r. equi and e. coli isolates were investigated in 200 samples of sand obtained from 40 parks, located in central region of state of sao paulo, brazil, using different diagnostic methods. from 200 samples analyzed, 23 (11.5%) strains of r. equi were isolated. none of the r. equi isolates showed a virulent (vapa gene) or intermediately virulent (vapb gene) profiles. sixty-three (31.5%) strains of e. coli were identified. the following genes encoding virulence factors were identified in e. coli: eae, bfp, saa, iucd, papgi, sfa and hly. phylogenetic classification showed that 63 e. coli isolates belonged to groups b1 (52.4%), a (25.4%) and b2 (22.2%). no e. coli serotype o157:h7 was identified. eggs of toxocara sp. were found in three parks and genetic material of bovine coronavirus was identified in one sample of one park. no salmonella spp. and rotavirus isolates were identified in the samples of sand. the presence of r. equi, toxocara sp, bovine coronavirus and virulent e. coli isolates in the environment of parks indicates that the sanitary conditions of the sand should be improved in order to reduce the risks of fecal transmission of pathogens of zoonotic potential to humans in these places. enteric pathogens are a major group of organisms related to infections in humans and animals. these pathogens are resistant to adverse environmental conditions and are frequently transmitted by oral route due to fecal contamina-risks posed by microorganisms eliminated in feces of animals favor the transmission of pathogens of animal origin to humans in these places (matsuo and nakashio, 2005) . the present study investigated the presence of pathogens of viral (coronavirus, rotavirus), parasitic (toxocara spp.) and bacterial (e. coli, salmonella spp., r. equi) origin eliminated in feces of animals, and the virulence profile of r. equi and e. coli isolates, obtained from the sand of parks located in the central region of state of sao paulo, brazil. two hundred samples of sand from 40 parks were analyzed. the strains were collected between 2008 and 2009. all parks were located in the central region of state of sao paulo, brazil. after superficial dirt was removed, about 250 g of soil were collected 10-15 cm deep. samples were placed in individual plastic bags and taken to laboratory under refrigeration (4-8°c). all samples were processed in the laboratory of microbiology and infectious diseases of animals, department of veterinary hygiene and public health, school of veterinary medicine, unesp -universidade estadual paulista, botucatu, sao paulo, brazil. samples were kept under refrigeration (4-8°c) or frozen (-20°c) until they were analyzed. samples (25 g) of feces from all parks were inoculated aseptically in 225 ml sterilized distilled water. after homogenization, 0.03 ml of material was inoculated in defibrinated bovine blood agar (5%) and macconkey agar for e. coli isolation. plates were incubated at 37°c for three days and were assessed every day for bacterial growth. simultaneously, 0.03 ml of these samples were cultured in nanat selective media for r. equi (takai et al., 1996) . microorganisms were identified by colony morphology, staining methods, and biochemical tests (quinn et al., 1994) . isolates of bacterial origin were stored in lignièris agar at 25°c. briefly, samples (25 g each) were inoculated into 250 ml of peptone water 1.0% (oxoid) and incubated at 35°c for 24 h. aliquots of 0.1 ml and 1 ml were inoculated each into 10 ml of rappaport-vassiliadis (rv) (oxoid) and tetrathionate (tt) (oxoid) broth, respectively, and incubated at 42°c (rv) and 35°c (tt) for 24 h. a loopful of each broth culture was inoculated simultaneously in xylose-lysine-desoxycholate agar (xld) (oxoid) and bismuth sulfite agar (bs) (oxoid), followed by incubation at 35°c for 24 h. colonies suggestive of salmonella were inoculated in triple sugar iron (tsi) and lysine iron (lia) agar slants. tubes were incubated for 35°c for 24 h. colonies suggestive of salmonella spp. in at least one of the culture media (tsi or lia) were submitted to biochemical tests, agglutination test using polyvalent anti-salmonella serum (probac) (quinn et al., 1994; andrews et al., 1998) , and serotype identification (popoff and le minor, 1992) . isolation of plasmid dna was obtained by using an alkalin lysis method (takai et al., 2003) . target dna for pcr amplification was based on the genes encoding a 15-17 kda antigen (vapa gene), and a 20 kda antigen (vapb gene) sequence. plasmid dna was digested with restriction endonucleases (ecori, ecot22i and hinddiii). primer 1 (5'-gactcttcacaagacggt-3') and primer 2 (5'-taggcgttgtgccagcta-3') were used to detect virulent (vapa gene) strains and the 569-552 bp expected product. primer 3 (5'-aacgtagtcgcggtgag aa-3') and primer 4 (5'-accgagacttgagcgacta--3') were used for intermediately virulent (vapb gene) isolates to detect the 1066-1048 bp expected product. samples were submitted to 30 cycles of amplification as follows: denaturation for 90 s at 94°c, annealing for 1 min at 55°c, and extension for 2 min at 72°c (takai et al., 1996; takai et al., 2003) . characterization of plasmid virulence was performed in kitasato university, japan. sorbitol-negative o157:h7 serotypes were submitted to agglutination test with o157 and h7 sera (probac). reference strains were e. coli fvl2 (sfa, pap, iucd, hly, cnf-1), fv35 (afa, iucd, cnf-1), j96 (papgii, papgiii), o157:h7 (vt1, vt2, eae), 2348/69 (eae, bfp, eaf), iano (stb, lt1), eaec o42 (eaec), b90 (cnf-2), fvl16 (cnf-1, hly, pap, sfa, iucd), etec13 (sta), eiec (ipah), supplied by the laboratory of bacterial antigens, campinas state university, brazil. e. coli dh5a strain was used as a negative control. first, primers for virulence factor genes were determined individually using a template dna from appropriate positive and negative control strains. the presence of the following groups of genes were analyzed by pcr: papc and papg alleles (p fimbria), sfac/d (s fimbria), afab/c (afimbrial adhesin), saa (self-agglutinating adhesin), iucd (aerobactin), cnf-1 and cnf-2 (cytotoxic necrotizing factor type 1 and 2), hly (a-hemolysin), vt1 and vt2 (verotoxins), sta and stb (heat stable toxins), lt1 (heat labile toxins), eaec (e. coli eaec), ipah (e. coli eiec), and eae, eaf and bfp (e. coli epec). appropriate primer sequences, annealing temperature, and size of amplified fragment (base pairsbp) for these genes were determined in previous studies (schmidt et al., 1995; yamamoto et al., 1995; blanco et al., 1996; blanco et al., 1997; karkkainen et al., 1998; aranda et al., 2004; villareal et al., 2006) . phylogenetic classifica-tion (chua, yjaa, tspe4.c2) in groups a, b1, b2 and d was performed by pcr (emödy et al., 2003) . flotation-centrifugation with sodium nitrate (na 2 no 3 ) 1.20 g/cm 3 was used for the recovery of toxocara spp. eggs. centrifugation was performed at 2.500 rpm (679 g) for 5 min. after that, the supernatant of each tube was placed in microscope slides, covered with coverslips, and examined under a light microscope (10x). this process was repeated three times for each sample (santarém et al., 1998) . samples were tested for the presence of bcov with a group ii coronavirus specific rt-pcr assay targeted to the rna-dependent rna-polymerase gene (rdrp) with a 136-bp predicted product (brandão et al., 2005) . bcov kakegawa strain (akashi et al., 1980) and pbs were used as positive and negative controls, respectively. samples were analyzed for the presence of rotavirus 11-segment rna using polyacrylamide gel electrophoresis-page (herring et al., 1982) . ncdv group a rotavirus strain was used as the positive control. chi-square test (epi-info, 6.4) was used to evaluate the differences in the presence of different pathogens in the parks, considering p <0.05 (triola, 2005) . the frequency of pathogens identified in samples of sand obtained from parks is shown in table 1 . there was no statistical difference (p >0.05) between the presence of the different pathogens in the parks sampled. e. coli and r. equi strains were the most common pathogens isolated throughout the study. r. equi strains were isolated in 23 (11.5%) sand samples. none of the r. equi isolates showed virulent (vapa gene) or intermediately virulent (vapb gene) plasmid profiles. sixty-three (31.5%) strains of e. coli were identified. the following virulence factor genes were identified in the e. coli strains: eae, bfp, saa, iucd, papgi, sfa and hly. phylogenetic classification showed that the 63 e. coli isolates belonged to groups b1 (52.4%), a (25.4%) and b2 (22.2%). no e. coli serotype o157:h7 was identified ( table 2) . eggs of toxocara spp. were recovered only in three of the parks. genetic material of bovine coronavirus was identified in one public park (table 1) , as suggested by the sequencing analysis of the 136 bp amplicon obtained in one sample (data not show). no salmonella spp. or rotavirus isolates were identified in the samples of sand. rhodococcus equi is a well-recognized gram positive intracellular bacterium associated with different clinical manifestations in humans and animals. the organism is widespread in soil, particularly in feces of foals, other herbivores and their environment (prescott, 1991) . the virulence mechanism of this pathogen is related with the presence of virulence-associated plasmids-vap (takai et al., 1991) , and three levels of virulence are currently recognized: virulent, intermediately virulent and avirulent (takai, 1997) . virulent r. equi strains contain a large plasmid of 85-90 kb, responsible for encoding the 15-17-kda antigens (vapa) that are considered the major causes of suppurative pneumonia in foals (ribeiro et al., 2005) . vapb or intermediately virulent isolates present 20-kda antigens and a 79-100 kb plasmid (takai, 1997) . they are frequently observed in swine lymphadenitis (takai et al., 1996) and patients infected by acquired immunodeficiency syndrome-aids (takai et al., 2003) . in contrast, avirulent strains show no evidence of either vapa or vapb genes. these strains are found in the soil of areas where foals are raised, in soil and/or sand of human dwelling, mainly in yards and parks, and in humans with rhodococcosis co-infected by aids virus (takai et al., 1996; takai, 1997) . all our r. equi strains were classified as avirulent. these results are in agreement with similar study in japan, which also reported the presence of avirulent r. equi in the soil of parks and yards (takai et al., 1996) . avirulent strains have been frequently identified in the environment of domestic animals, particularly foals (takai, 1997) . currently, r. equi has emerged as a pulmonary pathogen among immunosuppressed patients, mainly those infected by aids virus (acha and szyfres, 2003) . a recent survey of r. equi virulence profile in 20 humans in brazil showed 11 patients infected with avirulent strains (ribeiro et al., 2011) . plasmid virulence of r. equi strains isolated in brazil was characterized in foals (ribeiro et al., 2005) and a dog (farias et al., 2007) . the present study was the first investigation in this country about virulence profile of r. equi strains isolated from park sand. beside the absence of virulent or intermediately virulent r. equi strains, the presence of this microorganism in the sand of parks constitutes a public health problem. this risk is particularly important to children and immunocompromised people, especially hiv-positive patients, because avirulent r. equi may cause the disease in immunosuppressed and non-immunosuppressed patients (takai et al., 2003) , including in brazil (ribeiro et al., 2011) . e. coli is a very diverse species of bacteria found both in the intestinal tract of humans and animals, and in the environment. the microorganism is classified in six different pathotypes based on enteric manifestations, as follows: enterotoxigenic (etec), enteropathogenic (epec), enteroinvasive (eiec), enterohemorrhagic (ehec), enteroaggregative (eaec), and diffusely adherent (daec). pathogenic manifestations of e. coli are closely related with different virulence factors, including enterotoxins, cytotoxins, fimbriae, adhesins, and iron chelation mechanisms (kaper et al., 2004) . gene eae encodes intimin, which mediates the intimate attachment of epec and ehec to epithelial cells, and stimulates mucosal immune response and intestinal crypt hyperplasia. gene eae and bfp were found in three strains isolated from the sand of parks in the present study, and are generally related with atypic enteropathogenic e. coli. this class of e. coli epec causes diarrhea in children younger one year of age, mainly in emerging countries (kaper et al., 2004) . in brazil, there was a case of concurrent infection of a child and a dog by enteropathogenic e. coli that showed eae gene and was isolated from feces (rodrigues et al., 2004) . atypic epec isolated from parks constitutes a public health risk, especially for children and immunosuppressed humans. p fimbriae are known to contribute for e. coli pathogenesis by promoting colonization of host tissues and stimulating injurious inflammatory response in the host (kuehn et al., 1994) . papg adhesin is located on p fimbria. three classes of papg (papgi, papgii and papgiii) are recognized: papg class i are predominantly found in fecal strains; allele gii in strains involved in pyelonephritis and bacteremia cases; and allele giii in isolates responsible for cystitis cases in humans and animals (bergsten et al., 2005) . s pillus is constituted of subunits: sfas subunit mediates e. coli interaction with intestinal and other epithelial cells. sfas gene is associated with human pyelonephritis, meningitis and sepsis (féria et al., 2001) . haemolysin is a pore-forming cytotoxin that lyses erythrocytes, leukocytes, and endothelial and epithelial cells of mammals. the hly genes are frequently found in extraintestinal e. coli infections in humans and animals (johnson et al., 1991) . one of our isolates harbored the genes that encode papgi, sfa and hly. the identification of these virulence factors in a same isolate may be explained by the presence of a pathogenicity island (pai), which enhances the infectivity of the microorganism. pais have been frequently found in e. coli responsible for human extraintestinal infections (kurazono et al., 2000) . in brazil, genes that encode papg adhesins, as well as hly and sfa genes, were found in e. coli strains isolated from pyometra, urinary tract infections, and feces of dogs (siqueira et al., 2009) . free access of dogs to parks increases the risk of human infection with virulent e. coli. these animals may act as reservoirs, harboring pathogenic strains with virulence factors such as papg, hly, and sfa genes. iron is essential for bacterial metabolism. e. coli uses this ion for the transport and storage of both electrons and oxygen, and for dna synthesis (emödy et al., 2003) . growth of bacteria under restricted iron concentrations make them use successfully competitive mechanisms to obtain this ion from the host. aerobactin is the most effective iron chelation system employed by e. coli for iron acquisition, mediated by iuc genes types a, b, c and d (griffiths, 1997) . in humans, this virulence factor is intimately associated with urinary infections and septicemia (torres et al., 2001) . the iucd genes were found in only one isolate of our study. currently, iuc genes have been found in dogs with pyometra (coogan et al., 2004) , urinary tract infections, and in dog feces in brazil (siqueira et al., 2009) . like other virulence factors, the presence of iucd gene in e. coli strains isolated from sand represents a risk to the population visiting these parks. the presence of a self-agglutinating adhesin (saa) in e. coli has been previously described (paton et al., 2001) . virulence of this adhesin to humans and domestic animals remains unclear. however, saa gene was found in 19.0% of e. coli strains obtained from the sand of parks in the current study. this result suggests that further studies should be carried out in order to investigate the role of this adhesin as an e. coli virulence factor. e. coli have been phylogenetically classified in four groups named a, b1, b2 and d. e. coli strains belonging to groups b2 and d are commonly pathogenic for humans and animals, whereas a and b1 are less pathogenic (clermont et al., 2000) . based on phylogenetic systematics, e. coli isolates obtained from the sand of parks were classified in a and b1 groups. although these groups are predominantly related with non-pathogenic e. coli strains, these results indicate fecal contamination of the environment. toxocariasis is a cosmopolitan parasitic zoonosis. toxocara spp. is one of the most common parasites of young dogs and cats. eggs of the parasite are frequently shed in large amounts in the feces of companion animals. toxocariasis in human occur by spread of the larvae, leading to different clinical forms of disease. clinical manifestations involve serious neurological, ophthalmologic, pulmonary, and/or cutaneous signs (acha and szyfres, 2003) . the presence of eggs of toxocara spp. in the sand of parks have been reported in several countries (dubná et al., 2007; matsuo and nakashio, 2005) , including in brazil (santarém et al., 1998) . three parks had positive samples for eggs of this parasite. these results suggest environmental contamination by feces of companion animals and indicate risk of toxocariasis to humans that use these parks, particularly children. coronavirus infections in animals were reviewed elsewhere (brandão et al., 2001) . in brazil, previous studies have identified coronavirus in feces of cattle and dogs with and without diarrhea (brandão et al., 2005 (brandão et al., , 2007 . identification of bovine coronavirus in the sand from parks in brazil is uncommon, although it also represents fecal contamination of the environment. rotavirus was detected in the feces of domestic animals (rodriguez et al., 2004; ruiz et al., 2009) and chickens (villarreal et al., 2006) with and without diarrhea in brazil. likewise, different salmonella spp. serotypes were detected in feces of livestock (ribeiro et al., 2010) , birds and chickens (hofer et al., 1997) in this country. none of sand samples collected in our parks showed rotavirus and salmonella spp. in contrast, an epidemiological study involving human patients with salmonellosis in several european countries revealed that one the major risk factors for the disease was the access of children up to four years of age to the sand of parks (doorduyn et al., 2006) . these findings indicate that similar studies must be performed in other regions in brazil in order to investigate the occurrence of salmonella spp. and rotavirus in the sand of parks. despite the absence of salmonella spp. and rotavirus in the samples analyzed, these pathogens should be included in microbiological testing required to determine the sanitary conditions of the sand used in parks, as they may be shed in the feces of birds and domestic animals. the identification of r. equi, e. coli epec, bovine coronavirus, and toxocara spp. are indicators of fecal contamination of the sand of the parks sampled. contamination may have been caused by feces from domestic animals (takai et al., 1996) , birds (prescott, 1991) , or contaminated shoes of people who visit these places. our results suggest the need to introduce control measures to prevent contamination of the sand by pathogens eliminated in animal feces. in fact, the risks of the transmission of pathogens shed in animal feces in parks may reduce if access of domestic animals to these places is prevented, fecal material is daily removed from the sand, sand is periodically tested for sanitary quality and replaced with material of known origin, and people are continuously educated on hygiene habits before using parks. the presence of r. equi, e. coli epec, toxocara spp. and bovine coronavirus identified in parks studied indicates environmental contamination by microorganisms found in feces of domestic animals, birds, and/or contaminated shoes of people. these results represent a risk for the transmission of pathogens with zoonotic potential to humans in these places, particularly to children. zoonoses y enfermidades transmisibles comunes al hombre y los properties of a coronavirus isolated from a cow with epizootic diarrhea bacteriological analytical manual. food and drug administration evaluation of multiplex pcrs for diagnosis of infection wit diarrheagenic escherichia coli and shighella spp escherichia coli, fimbriae, bacterial persistence and host response induction in the human urinary tract polymerase chain reaction for detection of escherichia coli strains producing cytotoxic necrotizing factor type 1 and type 2 (cnf1 and cnf2) detection of pap, sfa and afa adhesin-encoding operons in uropathogenic escherichia coli strains: relationship with expression of adhesions and production of toxins a nested polymerase chain reaction to bovine coronavirus diagnosis animal coronaviruses winter dysentery in dairy cows associated with bovine coronavirus (bcov) rapid and simple determination of the escherichia coli phylogenetic group estudo microbiológico de conteúdo intra-uterino de cadelas com piometra e pesquisa de fatores de virulência em cepas de escherichia coli van pelt w (2006) risk factors for salmonella enteritidis e typhimurium (dt104 and dt104) infections in the netherlands: predominant roles for raw eggs in enteritidis and sandboxes in typhimurium infections contamination of soil with toxocara eggs in urban (prague) and rural areas in the czech republic virulence factors of uropathogenic escherichia coli cutaneous pyogranuloma in a cat caused by virulent rhodococcus equi containing an 87 kb type i plasmid distribution of papg alleles among uropathogenic escherichia coli isolated from different species iron and the virulence of escherichia coli rapid diagnosis of rotavirus infection by direct detection of viral nucleic acid in silver-stained poliacrylamide gels prevalência de sorovares de salmonella isolados de aves no brasil virulence factors in escherichia coli urinary tract infection pathogenic escherichia coli rapid and specific detection of three different g adhesin classes of p-fimbriae in uropathogenic escherichia coli by polymerase chain reaction genetic, biochemical, and structural studies of biogenesis of adhesive pili in bacteria characterization of a putative virulence island in the chromosome of uropathogenic escherichia coli possessing a gene encoding a uropathogenicspecific protein prevalence of fecal contamination in sandpits in public parks in sapporo city characterization of saa, a novel autoagglutinating adhesin produced by locus of enterocyte effacement-negative shiga toxigenic escherichia coli strains that are virulent for humans formules antigéniques des sérovars de salmonella. centre collaborateur oms de réference et de recherches pour les salmonella rhodococcus equi: an animal and human pathogen identification of virulence associated plasmids in rhodococcus equi in humans with and without acquired immunodeficiency syndrome in brazil molecular epidemiology of virulent rhodococcus equi from foals in brazil: virulence plasmids of 85-kb type i, 87-kb type i, and a new variant, 87-kb type iii caracterização de sorotipos em linhagens do gênero salmonella isoladas de diferentes afecções em animais domésticos. pesq vet bras concurrent infection in a dog and colonization in a child with a human enterophatogenic escherichia coli clone improved animal rotavirus isolation in ma-104 cells using different trypsin concentrations isolation of rotavirus from asymptomatic dogs in brazil contaminação por ovos de toxocara spp em parques e praças públicas de botucatu development of pcr for screening of enteroaggregative escherichia coli virulence factors in escherichia coli strains isolated from urinary tract infection and pyometra cases and from feces of dogs association between a large plasmid and 15-to 17-kilodalton antigens in virulent rhodococcus equi epidemiology of rhodococcus equi infections: a review isolation of virulent and intermediately virulent rhodococcus equi from soil and sand on parks and yards in japan this work was supported by fapesp -fundação de amparo à pesquisa do estado de são paulo, brazil (2007/57781-3) key: cord-345834-l2e5v39s authors: anacleto, m.a.; brito, f.a.; de queiroz, a.r.; passos, e.; santos, j.r.l. title: diffusive process under lifshitz scaling and pandemic scenarios date: 2020-08-20 journal: physica a doi: 10.1016/j.physa.2020.125092 sha: doc_id: 345834 cord_uid: l2e5v39s we here propose to model active and cumulative cases data from covid-19 by a continuous effective model based on a modified diffusion equation under lifshitz scaling with a dynamic diffusion coefficient. the proposed model is rich enough to capture different aspects of a complex virus diffusion as humanity has been recently facing. the model being continuous it is bound to be solved analytically and/or numerically. so, we investigate two possible models where the diffusion coefficient associated with possible types of contamination are captured by some specific profiles. the active cases curves here derived were able to successfully describe the pandemic behavior of germany and spain. moreover, we also predict some scenarios for the evolution of covid-19 in brazil. furthermore, we depicted the cumulative cases curves of covid-19, reproducing the spreading of the pandemic between the cities of são paulo and são josé dos campos, brazil. the scenarios also unveil how the lockdown measures can flatten the contamination curves. we can find the best profile of the diffusion coefficient that better fit the real data of pandemic. in december 2019, the world started to face a new type of severe pneumonia which appeared in wuhan, china. only two months later the international committee on taxonomy of viruses named the virus responsible for these pneumonia cases as severe acute respiratory syndrome coronavirus 2 or sars-cov-2, whose disease was popularly known as coronavirus disease 2019, or simply covid-19 [1] . such disease was classified as a public health emergency of international concern at the end of january 2020, by the world health organization. up to now, sars-cov-2 has spread all over the world, presenting more than 3.5 million of cases, taken approximately 247107 lives, and has a new epicenter in the united states of america which has reported almost one-third of the total amount of cases [2] . few places in the world were able to fully control the pandemic of covid-19. in europe, for instance, italy and spain were for a long time the world's two worst-hit countries by the covid-19. now, the numbers of active cases in these two countries are slowly decreasing and they are facing the final stage of the pandemic. one of the best countries in europe to adopt measures against covid-19 so far is germany, who is also entering in the controllable phase of the pandemic. behind the success of germany are measures of social distance or lockdown procedures, and a large number of people tested for sars-cov-2 [3] . after spreading in asia and europe, now covid-19 is a challenge for the usa, as well as for low and middle-income countries, such as brazil. there is a serious concern on the international scientific community about the behavior of sars-cov-2 in such countries, since they face other severe problems such as poverty, food security, economic growth, besides other diseases like human immunodeficiency virus, tuberculosis, and malaria [4] . so far, several scientific works and reports based on numerical simulations have been published, lighting the evolution of the pandemic in different countries and reflecting the actions as well as the strategies of each country to mitigate the effects of covid-19. some of these studies can be found in references [4] [5] [6] [7] [8] . among recent works on this subject, we also highlight an interesting proposal of an age-structured model presented by canabarro et al. [9] , a model based on hospital infrastructure developed by pacheco et al. [10] , and a study to predict covid-19 peaks around the world based on active cases curves, introduced by tsallis et al. [11] . in this work we intend to collaborate with the current investigations by proposing a model which can describe the evolution of the pandemic through the solutions of a modified version of the diffusion equation. the standard diffusion equation describes the macroscopic behavior due the effect of many micro-particle bodies, as it is observed in a brownian motion, for instance [12] . an interesting modification of this equation was proposed in the seminal paper of petr horava [13] , in his studies about quantum gravity, where he extended the definition of spectral dimension to theories on smooth spacetimes in anisotropic or lifshitz scaling. in our investigation, we introduce a new version of the diffusion equation inspired by horava's work, and we use it to fit real active cases data of covid-19 from germany, spain and brazil. the diffusion equation with the lifshitz scalling and the equation of motion for the diffusion coefficient are going to be introduced in section ii. in section iii we are going to show different solutions for the diffusion equation which can be used to fit the evolution of covid-19. the availability of our models are carefully discussed in section iv. the spreading of the pandemic between two different cities is modeled in section v. then, we present our final remarks and perspectives in section vi. the first issue to describe a pandemic evolution consists in choosing an appropriate diffusion process. the complexity of a virus transmission such as sars-cov-2, demands a diffusion process characterized by a probability density ρ = ρ(x, τ ; x , τ ; σ) measuring the diffusion from a time τ to a time τ , and from a space coordinate x to x at a diffusion time σ. notice that σ and τ are two different types of time, τ would be understood as the standard time variation of the pandemic, while σ would control the collective response to the pandemic, such as social distance measures, for instance. besides, as each country can adopt several strategies to mitigate the pandemic effects, it is expected that the diffusion process would account for different degrees of anisotropy. a general continuous diffusion equation that attends such criteria was introduced by horava in his seminal work [13] , whose form is here τ is the so-called euclidean time and z is the lifshitz critical exponent, which measures the anisotropic scaling of a given model [13, 14] . the lifshitz critical exponent is essential to determine the spectral dimension, which can be applied to several geometric objects presenting fractal behavior [13] . the relative sign (−1) z+1 concerns the requirement of ellipticity of the diffusion operator valid for integer z, but the results can be analytically continued for any positive real z [13, 14] . an extra relevant ingredient to proper modeling a pandemic spread is a diffusion coefficient, which can account for the transmission rate of the virus. therefore, this discussion suggests that a pandemic scenario is governed by the following anisotropic diffusion equation where φ(τ ) is a dynamic diffusion coefficient. we are going to show that a proper balance between φ and z yields to distributions that can fit real pandemic data. let us also constrain the diffusion coefficient φ(τ ) with the standard lagrangian where the negative kinetic part stands for the euclidean time. therefore, the equation of motion for the diffusion coefficient is such that by integrating the previous equation once, we find the first-order differential equation where we considered the function w is known as superpotential in analogy with the bosonic sector of a super symmetric field theory. the diffusion equation (2) has the general solution where ρ 0 stands for the initial probability density subject to the pandemic (or to the diffusion process). in this work, we consider ρ as the probability density of active cases of covid-19 to make a parallel between our model and real pandemic data. the number of active cases of covid-19 is defined as follows [3] active cases = total cases − total deaths − recovered , therefore, it represents the current number of patients detected and confirmed as infected with sars-cov-2. the number of active cases is also a relevant metric for public health and primary care functions, as it allows measuring capacity versus hospitalization needs. such a number is used to plot the distributions of active cases of covid-19 for different countries as we see in [3] , and it was used to predict the pandemic peaks in different countries as one can see in [11] . before starting to make numerical integrals of eq. (7) to depict the active cases curves, let us comment on the dimensionality of the model. a (spatial) bi-dimensional model seems most natural to discuss the diffusion process in the population. this usually is captured by the bi-dimensional networks with persons being nodes and relation being links [15] . moreover, one particular feature of the transmission of this virus is that it occurs by contact between persons [1] . this feature is captured by a nearest-neighbor interaction between the nodes. it can be argued that one can project down this nearest-neighbor interaction bi-dimensional network into a long-range interaction chain (one-dimensional chain) with appropriate boundary conditions. thus in the passing to the continuum model we can in a reasonable approximation consider a d = 1 model with x ranging from −∞ to +∞. for the numerical integration in the reciprocal space, we can take therefore −∞ ≤ ω ≤ ∞, and −∞ ≤ k ≤ ∞. moreover, we choose evaluate ρ at x = x indicating that the probability density is measured in the same spatial location after the evolution of the diffusion process. the simplest model that we can analyze consist in where the diffusion coefficient is normalized. this first model will enable us to observe the influence of the critical exponent and of the diffusion time in our curves. the fig. 1 shows four different behaviors for the solution of the diffusion equation. the diffusion time and the critical exponent z are competing parameters. particularly in the top left curve, with a same diffusion time large values of z ≥ 1 makes the gaussian flattened, whereas bottom right for z < 1 the gaussian tends to blow up even for sufficiently large diffusion time. the best scenario in the sense of flattening the gaussian curve seems to be the increasing of both diffusion time and critical exponent z (top right). the features of σ presented in the previous scenarios yield us to indeed understand the diffusion time as equivalent to a lockdown period. in this work we adopted the lockdown definition introduced by flaxman et al. [5] , which means a scenario where regulations and laws regard strict social interaction. these regulations/laws include the banning of any non-essential public gatherings, closure of educational, public and cultural institutions, and ordering people to stay at home apart from exercise or essential tasks. in this example we are going to consider the following superpotential where λ and α are real constants. such superpotential leads us to which is known as λ φ 6 potential, and it is depicted in the left panel of fig. 2 . the minima or vacua values of v correspond to φ v = 0, and φ v = ± √ 2 α. the region between these different minima is called a topological sector, and it mediates the transmission rate in our pandemic model. this potential was applied in subjects like higher-order phase transitions in ginzburg-landau theory [16, 17] , modeling domain walls in ferroelastic transitions [18] , and in new physics beyond the standard model of particles at high energies scales [19, 20] . the previous definition of w yields to the first-order differential equation whose analytic solutions are exhibiting anti-kink and kink-like profiles as one can see in figure 2 . once φ(τ ) can be interpreted as the transmission rate of the virus, in fig. 2 , we observe that for τ τ 1 the virus is not transmitted, however its transmission increases until an approximately constant rate (φ v = √ 2 α) as τ gets bigger than τ 1 . the applicability of such a model is going to be carefully discussed later, in section iv. as a next example, let us deal with a more complex model for the diffusion coefficient. such a model is derived from this potential is known as double sine-gordon model and it is applied to study ultra short optical pulses in he 3 [21, 22] , in decaying of false vacuum and phase transitions in field theory [22, 23] . the left panel of fig. 3 shows part of the periodic form of potential v (14). there we can see one topological sector between vacua φ v = ± n π/(2 κ). an interesting feature about this model is that the parameter β can deform this potential at φ = 2 π n/κ. such deformation is responsible for the double (anti)kink profiles observed in the right panel of fig. 3 , and it is also related to the variation of the transmission rate of our pandemic model. the previous potential yields to the first-order differential equation which is satisfied by the analytic solutions for s = ±1, and n = 0, ±1, ±2, ... . the behavior of these analytic solutions v can be appreciated in fig. there it is shown that φ(τ ) has three different regimes of transmission rate, the first one for τ τ 1 where φ v = (2 n − 1) π/(2 κ), the second regime occurs when τ ≈ τ 1 and φ ≈ π n/κ, and the third one appears for τ τ 1 and φ v = (2 n+1) π/(2 κ). these regimes can lead us to distributions with different waves of contagious, as we are going to show below. in the next section we are going to analyze the viability of model iii and compare the numerical curves of ρ derived from it with those obtained through model ii. as it is known, the active cases data can present a high level of uncertainty once it depends on the number of the tests performed by each country and also the countries' transparency in reporting the tests. the data set used to depict the graphics of this section were taken up to may 02, 2020. therefore, some discrepancies between our predictions and the pandemic evolution are expected. to depict active cases curves that could j o u r n a l p r e -p r o o f journal pre-proof reproduce the existent data and able to predict the behavior of the pandemic, we decided first to test our model against a now well-established data set, and for that, we choose data from germany. nowadays germany is the 6th leading country in the world in numbers of covid-19 cases, accumulating a total of 164967 cases up to may 02 [24] . moreover, germany is the third leading country in the total number of tests, reporting a total amount of 2547052 tests for sars-cov-2, which corresponds to 30400 tests per million of population (considering the data up to may 02) [24] . therefore, to constraint some free parameters in our model, we use the data from germany as guidance. despite this procedure, we still have other free parameters to represent the particular features of each country's strategy to deal with the pandemic. we present the features of our models against real active cases data from germany, brazil, and spain below. in this first scenario we shown in figs. 4, and 5, the active cases curves for germany integrated from model ii and iii, respectively. there, the black solid curves are the numerical solutions generated from eq. (7), which best fitted the real data depicted in blue dots. the parameters constrained in the fitting process were ρ 0 = 10 7 (for fig 4) , ρ 0 = 10 5 (for fig. 5) , and time scaling t = 2 τ representing the number of days of pandemic. moreover, we also used σ = 28 (for figs. 4, and 5), referring to the number of lockdown days in germany [25] . we also depicted the active cases data from germany (blue dots), since february 15, 2020 (day 1), until may 02, 2020 (day 78) [24] . the left panels of figs. 4, and 5 predict that the pandemic of covid-19 would be fully controlled in germany after day 102 of infection (or after may 26, 2020), when the number of active cases is less than 1000 people. besides, the active cases curves unveil that the kink and the double anti-kink solutions, eqs. (13) , and (16) deform the standard gaussian curve. by comparing the right panels of figs. 4, and 5, we realize that the double anti-kink solution yields us to a better fitting of real data, reproducing a change in the decreasing of the number of active cases at t ≈ 60 day. the graphics of figs. 6, and 7 shown the currently infected people by sars-cov-2 in spain. at the present moment, spain reported an amount of 245567 cases of covid-19, which makes it the second leading country in the world pandemic rank [26] . the active cases data for spain are depicted as blue dots in figs. 6, and 7, and to plot our numerical curves we considered σ = 43 lockdown days [25] . we can observe that the black solid curves are in good agreement with the pandemic data, and they predict that the active cases of covid-19 would be fully controlled in spain after day 120 (june 11, 2020), where the number of infected people is less than 1000. moreover, in this scenario the kink and the double anti-kink like solutions eqs. (13) , and (16), strongly deform the standard gaussian curve. as in the case of germany, the double anti-kink curve leads us to a better fitting of real data, reproducing a second wave of contagious after day 50. the pandemic of covid-19 starts in brazil eleven days after spreads in europe. despite this few difference in time, the evolution of the contamination in brazil was deeply different from germany and spain, as we can see in the graphics of figs. 8, and 9. the numerical solutions presented in figs. 8, and 9 were depicted using the same values for ρ 0 and t from germany curves and the same value for z from spain curves. moreover, we derived two possible scenarios of lockdown measures, the black solid curves show a model with σ = 30 lockdown days while the red solid curves were depicted with σ = 90 lockdown days. furthermore, we also included the active cases data from brazil as blue dots [27] . the real data from brazil reveal an abrupt change of contamination which started on day 48 (april 13, 2020) and developed to a new increasing rate after day 56 (april 26, 2020). along this period, besides the pandemic, brazil has been facing a political crisis, which would explain the behavior of the covid-19 infection here observed. another problem with brazil's data is its high degree of uncertainty. up to may 02, 2020, brazil reported a total of 97100 cases of covid-19, figuring at the 9th leading country in the world pandemic rank [3] . however, brazil has performed only 339552 tests of covid-19, representing a total of 1597 per million of people [3] . for these reasons, it is challenging to make any prediction about the evolution of the pandemic in brazil. although, our curves seem to be in good agreement with the active cases data so far, and we also can realize that a long time social distance flatten the curves of the active cases. the peaks of the two active cases curves from figs. 8, and 9 have considerable differences about 115000, and 141000 cases, respectively. moreover, the peaks are predicted to happen on days 92 (may 27, 2020), and 86 (may 21, 2020) for black and red solid curves from fig. 8 , and on days 95 (may 30, 2020), and 110 (june 04, 2020) for black and red curves from fig. 9 . it is relevant to mention, that up to may 02, 2020, brazil can attend in maximum 32703 patients with needs for icu [28] .the solutions from fig. 8 predict that the pandemic in brazil would not be fully controlled earlier than day 131 (june 22, 2020). in the longer predicted scenario, observed in the red solid curve of fig. 9 , the pandemic would be fully controlled after day 198 (august 28, 2020), when the number of active cases is less than 1000. we also realize that the double anti-kink like solutions are able to fit better the real data than the single kink-like ones, reproducing the increasing in the number of active cases after day 48. . the peaks of black and red curves are approximately 268000 and 153000 cases, respectively. we also depicted the active cases data from brazil (blue dots), since february 26 (day 1), 2020 until may 02, 2020 (day 67) [27] . as it is known the primary mechanism used by covid-19 to spread is through person-to-person contact. consequently, big cities favor the spreading of the virus to small centers, once they facilitate the mixing of people from different areas. moreover, their strategical positions close to airports and crossed by state roads, make such cities susceptible to rapidly spread the virus to innermost regions. this phenomenon of advancing of covid-19 into the countryside happened in several places in the world, such as around new york city and close to several metropolises from brazil. it was also modeled in several regions of brazil using a markov chain approach as one can see in the work of costa et al. [29] . in this section, we adapted our diffusion equation to describe the dissemination of the virus around different cities. in order to reproduce such a scenario, we rewrite our diffusion equation as (17) where n is the number of the cities, and j i (σ) are free sources of the diffusion process. the previous equations present the following general analytic solutions and the free sources should obey the conservation constraint the simplest definition for the sources is to work with j i (σ) = constant. in this application we are going to understand such sources as proportional to the basic reproductive rate at the beginning of the pandemic, commonly known as r 0 [30] . the basic reproductive rate is a non-dimensional quantity which measures the secondary cases of contamination produced by one case introduced in susceptible populations [31] . such a rate is a key ingredient in several mathematical models to describe pandemic scenarios, and any attempt to estimate its value is a real challenge. consequently, by working with an equivalence between j i and r 0 , our model suggests that the basic reproductive rate is changed between different cities as the pandemic evolves in a given region. to exemplify our methodology, let us consider two cities from brazil which experienced the phenomenon of the spreading of sars-cov-2 to innermost regions. the cities here considered are são paulo, and são josé dos campos. these two cities have about 12 million and 721 thousand of inhabitants, respectively, and they are approximately 100 km distant apart. they are experiencing the so-called yellow-phase of the reopening plan designed by the state of são paulo government, where people have access to public places such as parks, restaurants, and cultural events with limited capacity [32] . the pandemic started in são paulo at february 25 (day 1), and up to august 02, 2020 it accumulated more than 200000 cases with more than 9600 fatalities [33] . the first case of covid-19 in são josé dos campos was reported in march 18, 2020 and the city has been registered more than 17000 cases, besides 204 deaths up to august 02, 2020 [33] . moreover, the most recent basic reproductive rate estimated for the state of são paulo in the beginning of the pandemic is r 0 = 9.24 [34] . in such an j o u r n a l p r e -p r o o f application, the best model to fit the cumulative cases data from the two cities was model ii, therefore, the asymptotic behavior of ρ in eq. (18) is going to be proportional to the product j i φ v , corresponding to a kink like profile for the density distribution. so, in the following application, we choose to test our model against the cumulative cases data. then, let us consider n = 2 as the number of the cities, and whereρ 0 is a proportionality constant and r 0 is the basic reproductive rate. taking the previous ingredients into eq. (18) yield us to depict the graphics presented in fig. 10 . there, we consider labels i = 1, and i = 2 to describe são paulo and são josé dos campos, respectively, and we worked with σ = 6 lockdown days, corresponding to the anticipation of holidays in the city of são paulo [35] . such anticipation of holidays was planned to increase the social distancing, attempting to reduce the spreading of covid-19. we can observe that our model successfully reproduces the evolution of the pandemic in theses two cities if we consider z = 50, which is the same value used to fit spain and brazil's active cases curves in the previous section. moreover, the fact that j 2 = −r 0 means that the basic reproduction rate was passing from são paulo to são josé dos campos between february 25 and march 18, as the pandemic spreading evolves. x = x , ρ 0 = 10 2 , α = 2.90 × 10 3 , s = 1, λ = 0.72 × 10 −1 , z = 50, τ = 50, τ 1 = 69, j 1 = 9.24,ρ 0 = 1, and σ = 6 (black solid curve). we also depicted the cumulative cases data from the city of são paulo (blue dots), since february 25 (day 1), 2020 until august 02, 2020 (day 160) [33] . in the right panel we present the cumulative cases solutions for model ii with t = 2τ (time in days), d = 1, x = x , ρ 0 = 10, α = −117.38, s = 1, λ = 0.82 × 10 −1 , z = 50, τ = 85, τ 1 = 77.5, j 2 = −9.24,ρ 0 = 1, and σ = 6 (red solid curve). besides, we depicted the cumulative cases data from the city of são josé dos campos (blue dots), since march 18 (day 1), 2020 until august 02, 2020 (day 137) [33] . in this work we introduced a modified version of the diffusion equation, mediated by a lifshitz scaling together with the diffusion coefficient φ(τ ). the diffusion time σ is analogous to the so-called fictitious time in stochastic quantization theories [36] . we were able to find an analytic solution for this diffusion equation, and to use the standard gaussian curves to interpret σ as the lockdown time, if such an equation is applied to model pandemic cases. therefore, we investigate two possible models with φ(τ ) having (anti)kink, and double (anti)kink-like profiles. these models were used to fit real active cases data of covid-19 from three different countries (germany, spain, and brazil). we successfully depicted the active cases curves for germany and spain up to may 02, 2020, and use them to constraint some of our free parameters to generate curves for brazil. then, we predicted four scenarios for the advance of the pandemic in brazil, based on 30 and 90 lockdown days. these scenarios alerted for a potential escalation of the pandemic in brazil if no lockdown measure is taken. moreover, the solution which best fitted the active cases data up to may 02, 2020, is the red curve from fig. 9 , where it was considered 90 lockdown days. such a solution predicted that the pandemic would be fully controlled after day 198 (august 28, 2020). from the previous analyses we are able to observe how crucial the lockdown measures are to flatten the active cases curves and to control the pandemic spread, corroborating with the remarks from [9] . we also applied our model in a new phase of the pandemic, where the virus is moving towards innermost regions of the countries. in this application we considered several diffusion processes interacting through free sources. each one of these diffusion processes corresponds to the spreading of sars-cov-2 in a given city. as a simplest case to model, we worked with constant sources and understood them as proportional to the so-called basic reproductive rate at the beginning of the pandemic (r 0 ). in order to exemplify our model we built the cumulative cases curves of two cities from brazil -são paulo and são josé dos campos, and compare them with real data. our results unveil that this pandemic model can be successfully applied in the context of coupled spreading of covid-19. it is relevant to point that the lifshitz scaling exponent was essential to depict the numerical curves here studied. moreover, we also verified that the double (anti)kink-like profiles were able to fit better the real active cases data than the single (anti)kink-like solutions. consequently, we can conjecture that multiple anti(kink)-like models, like those introduced in [37] , would improve the level of precision of our active cases curves, and would enable us to model multiple pandemic phases. another interesting perspective consists in investigate solutions for the diffusion equation derived from models with multiple lump like solutions, such as those presented in [38] . moreover, the methodology here adopted can be applied to other pandemics, as well as to other covid-19 data set like new daily cases, for instance. covid-19 dashboard the potential impact of the covid-19 epidemic on hiv, tb and malaria in low-and middle-income countries report 13 -estimating the number of infections and the impact of non-pharmaceutical interventions on covid-19 in 11 european countries contacts in context: large-scale setting-specific social mixing matrices from the bbc pandemic project expected impact of covid-19 outbreak in a major metropolitan area in brazil data-driven study of the covid-19 pandemic via age-structured modelling and prediction of the health system failure in brazil amid diverse intervention strategies coronavirus disease 2019 (covid-19) dynamics considering the influence of hospital infrastructure double sine gordon model, in solitons, topics in current physics germany: active coronavirus cases what are the lockdown measures across europe? spain: active coronavirus cases brazil: active coronavirus cases ministério da saúde covid-19 info metapopulation modeling of covid-19 advancing into the countryside: an analysis of mitigation strategies for brazil evaluating reduction in covid-19 cases by isolation and protective measures in são paulo state, brazil, and scenarios of release stochastic quatization we inform the credit statements about the preparation of this manuscript bellow • m.a. anacleto conceptualization, writing -review & editing, and brito conceptualization, investigation, writing -original draft, writing -review & editing, resources, supervision, and project administration de queiroz conceptualization, investigation, writing -original draft, writing -review & editing, and project administration passos conceptualization, writing -review & editing, and project administration we would like to thank cnpq, capes and pronex/cnpq & paraiba state research foundation (grants no. 165/2018 and 0015/2019), for partial financial support. maa, fab, ep and jrls acknowledge support from cnpq (grant nos. 306962/2018-7, 312104/2018-9, 304852/2017-1 and 420479/2018-0, respectively). the authors also would like to thank the anonymous referees for thoughtful comments which undoubtedly raised the quality of this work. key: cord-354699-u4s2r8gy authors: de souza, carlos dornels freire; machado, michael ferreira; do carmo, rodrigo feliciano title: human development, social vulnerability and covid-19 in brazil: a study of the social determinants of health date: 2020-08-31 journal: infect dis poverty doi: 10.1186/s40249-020-00743-x sha: doc_id: 354699 cord_uid: u4s2r8gy background: coronavirus disease 2019 (covid-19) was confirmed in brazil in february 2020. since then, the disease has spread throughout the country, reaching the poorest areas. this study analyzes the relationship between covid-19 and the population’s living conditions. we aimed to identify social determinants related to the incidence, mortality, and case fatality rate of covid-19 in brazil, in 2020. methods: this is an ecological study evaluating the relationship between covid-19 incidence, mortality, and case fatality rates and 49 social indicators of human development and social vulnerability. for the analysis, bivariate spatial correlation and multivariate and spatial regression models (spatial lag model and spatial error models) were used, considering a 95% confidence interval and a significance level of 5%. results: a total of 44.8% of municipalities registered confirmed cases of covid-19 and 14.7% had deaths. we observed that 56.2% of municipalities with confirmed cases had very low human development (covid-19 incidence rate: 59.00/100 000; mortality rate: 36.75/1 000 000), and 52.8% had very high vulnerability (covid-19 incidence rate: 41.68/100 000; mortality rate: 27.46/1 000 000). the regression model showed 17 indicators associated with transmission of covid-19 in brazil. conclusions: although covid-19 first arrived in the most developed and least vulnerable municipalities in brazil, it has already reached locations that are farther from large urban centers, whose populations are exposed to a context of intense social vulnerability. based on these findings, it is necessary to adopt measures that take local social aspects into account in order to contain the pandemic. in january 2020, a new coronavirus called severe acute respiratory syndrome coronavirus 2 (sars-cov-2) was identified, causing coronavirus disease 2019 (covid-19) [1] . on march 11, 2020 the who declared a pandemic [2] . as of april 11, 2020, there were more than 4.1 million cases and 284 000 deaths due to the disease worldwide [3] . the countries with the highest number of cases are the usa (1 300 000), spain (224 000), and the united kingdom (224 000). in number of deaths, the usa (79 000), the united kingdom (32 000), and italy (30 000) have the highest numbers [3] . in brazil, the first case of covid-19 was confirmed on february 26, 2020, and the first death was confirmed on march 17, in são paulo, the country's most populous metropolis, with approximately 12 million inhabitants [4] . the disease spread rapidly to other brazilian states. on april 11, 2020 the country had 163 000 cases and 11 000 deaths [3] , with confirmed cases in all 26 states and in the federal district. in all countries, but especially in those of low and middle incomes, there is concern regarding the effects of the pandemic on the most impoverished populations [5, 6] . these population groups have difficulties in adopting preventive measures (such as social isolation); they are exposed to a context of pragmatic vulnerability that increases the risk of contamination, and, if infection occurs, they have limited access to health services. this is a complex, dynamic context that requires special attention from governments. all of these conditions in which people live and which express, to a greater or lesser extent, the risk of illness, are called social determinants of health (sdh) [7] . the identification of the sdh that influence the dynamics of covid-19 in brazil is of fundamental importance for dealing with the pandemic and its consequences, thus contributing to the definition of mitigating public policies. in brazil, the human development atlas and the social vulnerability atlas are two important sources for studying the sdh, as they help to understand the context of the population's living conditions and thus supporting decision making. these include the municipal human development index (mhdi) and the social vulnerability index (svi) with their respective dimensions. the mhdi considers development as "the capacity to expand the freedoms of individuals, in relation to their capacities and opportunities" [8] . although advances have been observed, especially in the last three decades, the mhdi of 1/4 of brazilian municipalities are considered low or very low. the svi, on the other hand, measures "the access, absence, or insufficiency of some assets in areas of brazilian territory, which should, in principle, be available to every citizen, due to the action of the state." about 1/3 of the brazilian municipalities are classified as having high or very high vulnerability [9] . the mhdi ranges from 0 to 1; the closer to 1, the greater the degree of human development in the municipality. municipalities are classified into the following five development strata: very low (mhdi 0 to 0.499), low (mhdi 0.500 to 0.599), medium (mhdi 0.600 to 0.699), high (mhdi 0.700 to 0.799), and very high (mhdi 0.800 to 1) [8] . the svi varies from 0 to 1; the closer to 1, the greater the degree of social vulnerability in the municipality. municipalities are classified into the following five strata of vulnerability: very low (svi 0 to 0.200), low (svi 0.201 to 3.00), medium (svi 0.301 to 0.400), high (svi 0.401 to 0.500) and very high (svi > 0.501) [9] . based on this and on the need to understand the relationship between covid-19 and the population's living conditions, this study aimed to identify the sdh related to the incidence, mortality, and case fatality rates of covid-19 in brazil, in 2020. this is an ecological study involving all confirmed cases of covid-19 in brazil until may 6, 2020. in this study, the following three epidemiological indicators were adopted as dependent variables: i) covid-19 incidence rate/100 000 inhabitants, ii) covid-19 mortality rate/1 million inhabitants, and iii) covid19 in addition to these, the following 16 variables that make up the social vulnerability atlas and that express the population's living conditions were included: 1) illiteracy rate of people 18 years or elder, 2) illiteracy rate of people 25 years or elder, 3) income per capita of those vulnerable to poverty, 4) percentage of income from work, 5) gini index, 6) percentage of employees 18 years or older with a formal contract, 7) percentage of employees 18 years or elder without a formal contract, 8) percentage of public sector workers 18 years or elder, 9) percentage of self-employed workers 18 years or elder, 10) percentage of employers 18 years or elder, 11) degree of formality of the employed 18 years or elder, 12) percentage of employed persons 18 years or elder who have completed primary education, 13) percentage of employed persons 18 years or elder who have completed secondary education, 14) percentage of employed persons 18 years or older who have completed higher education, 15) average income of employed persons 18 years or elder, and 16) percentage of employed persons 18 years or elder without income. after data extraction, the variables were grouped into 10 blocks for statistical treatment. this organization aimed to reduce multicollinearity, which could compromise the quality of the study results. data analysis was subsequently divided into the following four stages: step 1-exploratory analysis of epidemiological indicators according to population size and human development and social vulnerability: in this stage, municipalities were grouped according to population size and strata of human development and social vulnerability. epidemiological indicators were subsequently calculated for each stratum, and exploratory analysis of rates was carried out. step 2-analysis of bivariate spatial correlation: moran bivariate statistics and pseudo-significance test were used to assess the correlation between the incidence rate and the independent variables. the moran index ranges from − 1 to + 1. values close to zero indicating spatial randomness; positive values suggest positive spatial autocorrelation, and negative values suggest negative spatial autocorrelation [10] . only variables with statistical significance (p < 0.05) in this stage were included in the next one. it should be noted that, in stages 2 and 3, only incidence rate was analyzed, given that only 821 municipalities (14.7%) had registered deaths on the date of collection. step 3 multivariate analysis and spatial association: the association between the covid-19 incidence rate and the independent variables was initially tested with the use of classical multivariate regression (ordinary least squares [ols]). the model residues were submitted to spatial dependence analysis by global moran statistics to assess the need to incorporate a spatial component of the regression model, according to the decision model proposed by luc anselin [11, 12] . once established, lagrange multiplier tests were applied to define whether the most appropriate spatial model for the data set would be the spatial delay model (assigning an unknown value to the response variable y) or the spatial error model (considering the spatial component as noise to be removed) [11] . finally, residues from spatial models were subjected to moran statistics again to verify spatial independence. in addition to this criterion, the following items were used to assess the quality of the final model: akaike information criterion (aic), bayesian information criterion (bic), log probability, and determination coefficient (r 2 ). analyses were performed using geoda software (version 1.10.0.8, university of illinois, urbana-champaign, usa). because this study uses data in the public domain, research ethics committee approval was waived. a total of 125 186 cases and 8452 deaths from covid-19 were included in the study. cases were reported in 2496 municipalities (44.8%), and deaths were reported in 821 municipalities (14.7%). although the disease is present both in municipalities with large populations (> 100 000 inhabitants) and in those with small sizes (≤ 10 000), 81.3% of municipalities with up to 10 000 inhabitants have not yet registered cases of covid-19. municipalities with populations over 100 000 inhabitants were the first affected, and, to date, they have an incidence of 88.95/100 000 and a mortality rate of 61.36/1 million inhabitants. in second place are municipalities with up to 10 000 inhabitants, with incidence rate of 45.89/100000 and mortality rate of 27.26/1 million. it is noteworthy that the case fatality rate in municipalities with populations between 10 000 and 20 000 inhabitants is similar to that observed in large municipalities (6.81 and 6.90%, respectively) ( table 1) . in relation to human development, it was observed that all 44 municipalities with very high mhdi were affected by covid-19. this group had the highest covid-19 incidence rate (106.71/100 000) and mortality (73.12/1 million). in second place are municipalities with very low mhdi, 56.2% of which have already registered cases of the disease. regarding incidence and covid-19 mortality rate, the group with very low mhdi held third place (covid-19 incidence rate: 59.00/100000 and covid-19 mortality rate: 36.75/1 million) (tables 1 and 2) . regarding social vulnerability, 55.8% of the municipalities with very low svi have already registered cases of covid-19, followed by the municipalities with very high svi (52.8%). considering the incidence and mortality rates, municipalities with average svi held first place (99.37 cases/100 000 and 68.48 deaths/1 000 000). it is also noteworthy that the municipalities with high svi had higher case fatality rate (7.36%) (tables 1 and 2) . initially, a positive bivariate spatial correlation was observed between the incidence rate of covid-19 and the general svi (moran i = 0.076; p = 0.002) and a negative correlation with the mhdi (moran i = -0.022; p = 0.002) (fig. 1) . of the 49 variables analyzed, five showed no spatial correlation with the incidence rate of covid-19 and were excluded from subsequent analyses. in the multivariate regression model, 21 variables were associated with incidence rate. none of the variables in block 2 (domains of the svi) showed significance. in all other blocks of variables, the residuals of the regression model were spatially dependent. lagrange multiplier tests indicated the spatial error model for block 8 (domains of the mhdi education) and spatial lag model for the others ( table 3) . the spatial regression model, finally, identified 17 indicators associated with incidence rate, 13 of which showed positive association, namely the following: svi; mhdi; mhdi education; percentage of people who live in households with per capita income less than half minimum wage (2010) and who spend more than 1 h to reach place of work; percentage of people aged six to 14 years who do not attend school; percentage of people aged 15 to 24 years who do not study, do not work, and have per capita household income equal to or less than half the minimum wage (2010); percentage of people with per capita household income equal to or less than half minimum wage (2010); activity rate of people aged 10 to 14 years; life expectancy at birth; percentage of individuals aged 11 to 13 who are enrolled in the final years of elementary school or who have completed elementary school; per capita income; percentage of employed persons aged 18 or elder with complete elementary school; and average income of employed persons aged 18 or over. four variables showed a negative association, namely, illiteracy rate of the population aged 15 years or over; percentage of employers aged 18 or over; percentage of people aged 18 or over without complete elementary education holding informal occupation; and percentage of employed people aged 18 or over with complete higher education (table 3 ). covid-19 currently represents the main global health, social, and economic challenge. in brazil, the spread of the disease started in the most developed municipalities in the country, and it has spread throughout the brazilian territory without delay, reaching smaller and more vulnerable areas whose populations are exposed to a chronic and historical context of social deprivation. this process of spatial dissemination justifies the complex influence of sdh on the spread of the virus across the country. considering that the virus is reaching the most vulnerable and least developed municipalities in the country after those with better living conditions, there is reason to believe that these municipalities will be more severely affected and will suffer incalculable consequences, if consistent support measures are not adopted urgently. the first reason concerns the risk context of these populations and the difficulties in implementing and/or adopting preventive measures. approximately 37 million brazilian workers earn their income from activities related to the sale of products and the provision of services, constituting a population vulnerable to contamination [13] . in poorer municipalities, the percentage of these populations rises considerably [13] . furthermore, in many cases, this is the only source of income for the family's subsistence, which makes adherence to voluntary social isolation difficult to maintain for a long period without the proper support of emergency public policies. covid-19, therefore, has a double effect on the most vulnerable populations, to the extent that it both perpetuates poverty and is perpetuated by poverty itself. it is perpetuating in the sense that, for each percentage point reduction in the global economy, it is estimated that an additional 10 million people will be placed in poverty [5] . in brazil, the pandemic could increase by 6.5 percentage points in the poverty index, thus affecting almost one quarter of the brazilian population [14] . it would furthermore increase inequality in income distribution (6.5% increase in the gini index) [14] . in the states of the north and northeast regions, these effects of pandemics can be even more pronounced, given that they are the least developed regions with the most vulnerable populations. it is perpetuated by poverty, because this vulnerable population, having no financial reserves and depending on emergency government assistance, will scarcely be able to adhere to non-pharmacological preventive measures, such as social isolation, wearing masks, and hand hygiene. in this regard, living conditions are able to maintain the covid-19 transmission chain active. in our study, there was a higher incidence rate in municipalities with greater social vulnerability; higher proportion of people who live in households with per capita income less than half minimum wage and who spend more than 1 h to reach place of work; higher proportion of children aged six to 14 years who do not attend school; and higher proportion of people aged 15 to 24 years who do not study, do not work and have a per capita income of less than half minimum wage. these populations are more likely not to follow government recommendations [15] . the lack of home structure and the lack of access to minimum resources, such as water and basic sanitation, both on the outskirts of large cities and in municipalities in the interior of the country, can increase the risk of illness due to covid-19, as observed with other respiratory diseases [16] . in brazil, four million families do not have a bathroom at home; 35 million do not yet have access to treated water, and 100 million do not have a sewage network [17] . therefore, it is possible to state that the degree of suffering generated by the pandemic depends on the area where individuals live and the social conditions to which they are subjected [18] . even in rich countries, such as the united states of america (usa), the social inequalities that exist in cities determine the greater or lesser risk of illness for their residents. in boston, for example, there is a high concentration of poverty and a prevalence of diseases caused by it in certain areas and good living conditions and a low prevalence of these diseases in other nearby points [19, 20] . this scenario reinforces the relationship between social policies and the health conditions experienced by the population. a study carried out in the usa, with data from 433 cities, involving 283 256 cases and 6644 deaths from covid-19, showed that the highest social vulnerability index was associated with a higher incidence and lethality due to the disease (relative risk-rr = 1.19), being still higher when considering the population aged 65 or older (rr = 1.63). in the study, 28.9% of the municipalities had a high social vulnerability (svi ≥ 0.46) and a high adjusted lethality rate (≥ 2.3%) [21] . in addition, mortality caused by the disease, especially in household providers, can increase the poverty of families. in this investigation, municipalities with small population sizes, as well as those with low mhdi and high svi already show high mortality rates. the situation tends to become more critical when all municipalities are affected, which will not take long to happen. even with the set of actions implemented by the brazilian government, through "brazil's response policy to covid-19" [22] , it is likely that after this pandemic, brazil will face a second crisis related to poverty and the diseases associated therewith. the loss of income can bring other consequences for the health of the population, such as a higher frequency of mental illnesses, increased consumption of alcohol and other drugs and increased domestic violence [23] . it is not yet possible to predict the size of the impact of the pandemic on people's lives, especially on the most vulnerable and, for this reason, strategies to combat covid-19 must be developed on different fronts of action. the second reason refers to the capacity of municipalities to face the contamination of their population and to offer conditions for detection and treatment of patients. if we consider that 7% of those infected will need hospitalization and that 2% will require intensive care [24] , the group of municipalities with very high vulnerability (which recorded 4964 cases of covid-19) would need 347 hospital beds and 99 intensive care unit (icu) beds. several factors make this scenario even more worrying. first, these small and more vulnerable municipalities do not have a hospital structure or icu beds to meet the demand imposed by the pandemic [25] . in general, these beds are concentrated in municipalities that are regional health centers that serve the municipalities through agreements between managers. second, because the disease first arrived in the larger municipalities with higher human development, these beds are already occupied. third, these populations depend exclusively on beds in the public unified health system (sus, acronym in portuguese). about 94.4% of the individuals who constitute poorest 20% of the population are dependent on the sus [21] . for this reason, the strengthening of all components of the health system is of fundamental importance for tackling the pandemic in brazil [26, 27] . even with all the precautions adopted, this study has some limitations, among which the following stand out: i. the underreporting of covid-19 cases due to the limited availability of tests and the capacity of local surveillance services, ii. deficiencies in investigating deaths due to the disease, with significant underreporting, and iii. use of secondary data that are subject to constant variation. concerns with the advance of the covid-19 pandemic in the country's smallest, most vulnerable, and least developed municipalities raise the alert for brazilian political authorities. it is necessary to do the following: 1) delay the arrival of the disease in these locations by adopting effective prevention mechanisms that consider the collective risk of illness, the social context experienced by these populations, and the best existing scientific evidence; 2) expand and prepare the health network with urgent investments in the sus at all levels of care; and 3) guarantee social protection for the vulnerable population. a novel coronavirus from patients with pneumonia in china covid-19): situation report -51. geneva: world health organization boletim epidemiológico do centro operações de emergência em saúde pública -doença pelo coronavírus 2019. brasil: ministério da saúde how much will global poverty increase because of covid-19 why inequality could spread covid-19 determinantes sociais da saúde vs determinação social da saúde: uma aproximação conceitual atlas de desenvolvimento humano no brasil. brasil: programa das nações unidas para o desenvolvimento -pnud, instituto de pesquisa econômica aplicada -ipea, fundação joão pinheiro -fjp brasil: instituto de pesquisa econômica aplicada -ipea análise espacial de dados geográficos. brasília: embrapa visualizing multivariate spatial correlation with dynamically linked windows using exploratory spatial data analysis to leverage social indicator databases: the discovery of interesting patterns perfil dos municípios brasileiros: saneamento básico: aspectos gerais da gestão da política de saneamento básico simulações de impactos da covid-19 e da renda básica emergencial sobre o desemprego, renda, pobreza e desigualdade low health literacy prevents equal access to care infecções respiratórias de importância clínica: uma revisão sistemática os efeitos sobre grupos sociais e territórios vulnerabilizados das medidas de enfrentamento à crise sanitária da covid-19: propostas para o aperfeiçoamento da ação pública (nota técnica n. 33). brasil: diretoria de estudos e políticas do estado, das instituições e da democracia covid-19's economic pain is universal investing in social services for states' health: identifying and overcoming the barriers covid-19 and the social determinants of health impact of social vulnerability on covid-19 incidence and outcomes in the united states. medrxiv: the preprint server for health sciences policy responses to covid-19. brasil: ministério da economia social determinants of health and inequalities in covid-19 preliminary estimates of the prevalence of selected underlying health conditions among patients with coronavirus disease 2019 united states necessidades de infraestrutura do sus em preparo à covid-19: leitos de uti, respiradores e ocupação hospitalar (nota técnica n. 3). instituto de estudos para políticas de saúde 2020 the need to strengthen primary health care in brazil in the context of the covid-19 pandemic primary health care in the confrontation with covid-19: analysis of the northeastern state contingency plans not applicable. authors' contributions cdfs, rfc, mfm reviewed and edited. were responsible for data management, analysis and quality control. the author(s) read and approved the final manuscript. availability of data and materials not applicable.ethics approval and consent to participate not applicable. not applicable. the authors declare that they have no competing interests. key: cord-261228-o80y5cic authors: jorge, d. c. p.; rodrigues, m. s.; silva, m. s.; cardim, l. l.; silva, n. b. d.; silveira, i. h.; silva, v. a. f.; pereira, f. a. c.; pinho, s. t. r.; andrade, r. f. s.; ramos, p. i. p.; oliveira, j. f. title: assessing the nationwide impact of covid-19 mitigation policies on the transmission rate of sars-cov-2 in brazil date: 2020-06-28 journal: nan doi: 10.1101/2020.06.26.20140780 sha: doc_id: 261228 cord_uid: o80y5cic covid-19 is now identified in almost all countries in the world, with poorer regions being particularly more disadvantaged to efficiently mitigate the impacts of the pandemic. in the absence of efficient therapeutics or vaccines, control strategies are currently based on non-pharmaceutical interventions, comprising changes in population behavior and governmental interventions, among which the prohibition of mass gatherings, closure of non-essential establishments, quarantine and movement restrictions. in this work we analyzed the effects of 547 published governmental interventions, and population adherence thereof, on the dynamics of covid-19 cases across all 27 brazilian states, with emphasis on state capitals and remaining inland cities. a generalized seir model with a time-varying transmission rate (tr), that considers transmission by asymptomatic individuals, is presented. confirmed covid-19 cases were used to calibrate the model parameters using non-linear least squares methods. we analyze the changes on the tr and effective reproduction number as a function of both the extent of enforced measures across brazilian states as well as population movement. the social mobility reduction index, a measure of population movement, together with the stringency index, adapted to incorporate the degree of restrictions imposed by governmental regulations, were used in conjunction to quantify and compare the effects of varying degrees of policy strictness across brazilian states. our results show that population adherence to social distance recommendations plays an important role for the effectiveness of interventions, and represents a major challenge to the control of covid-19 in lowand middle-income countries. duction number as a function of both the extent of enforced measures across brazilian states as well as population movement. the social mobility reduction index, a measure of population movement, together with the stringency index, adapted to incorporate the degree of restrictions imposed by governmental regulations, were used in conjunction to quantify and compare the effects of varying degrees of policy strictness across brazilian states. our results show that population adherence to social distance recommendations plays an important role for the effectiveness of interventions, and represents a major challenge to the control of covid-19 in low-and middle-income countries. keywords: brazil; covid-19; mathematical modeling; non-pharmaceutical interventions; transmission rate. covid-19, a disease caused by the sars-cov-2 coronavirus, emerged in december 2019 in china and was recognized as a pandemic by the world health organization on march 11, 2020 [1] . at that moment, brazil had already confirmed 53 cases. on march 20, with 972 confirmed cases, the brazilian ministry of health recognized community transmission of covid-19 throughout the national territory, 24 days after the first confirmed case of covid-19 was identified [2] . brazil is a country with 209.5 million individuals and stark socioeconomic disparities throughout its territory. it is the largest country in south america and the fifth largest nation in the world. accordingly, the many challenges imposed by the covid-19 pandemic are unprecedented in this country. the political-administrative organization of brazil comprises three spheres of governance: the union (federal government), the 27 states (including the federal district, where the capital city, brasilia, is located) and 5,570 municipalities. to reduce the transmission of sars-cov-2, federal, state and city governments implemented a series of interventions by means of government decrees [3] . this included recommendations to identify and isolate confirmed cases and contacts; to restrict unnecessary movements; to practice social distancing; to increase hygiene awareness; to follow respiratory etiquette; to widespread use masks, among others. in the absence of more intensive mitigation policies implemented by the federal government (such as lock-downs and movement restrictions), most measures were adopted by local governments (state/municipalities) [3] . however, adherence to these policies varied greatly throughout the country, and while some regions enacted more strict controls, others have been more lax. mathematical modeling has been instrumental to inform policies and to evaluate the trends of the covid-19 pandemic [4, 5, 6, 7, 8, 9] . here we define the transmission rate (tr) in terms of a generalized seir model, that simulates the dynamics of virus spread in a population entirely susceptible to the new virus. in this approach, the tr represents the probability that an infected individual will transmit the disease to a susceptible individual [10] . therefore, the higher this rate, the greater the number of new cases for a region. downward changes on the tr are expected with the implementation of mitigation policies such as non-pharmaceutical interventions (npi), currently the only option to limit the spread of sars-cov-2 given the absence of vaccines or effective therapies. in this work, we comparatively analyze the evolution of the covid-19 transmission rate and reproductive number in all 27 brazilian states, with emphasis on state capitals and remaining inland cities, establishing links with measures of governmental restrictions (npis) implemented in each region together with the human behaviour response, particularly the adherence to recommendations of social distancing. the varying degree of enforced policies across the country offers an opportunity to study the impacts of interventions, including their breadth and timing, on the tr of sars-cov-2 throughout brazilian states. these findings can be extrapolated to similar settings in other low-and middle-income countries to drive improvements in mitigation policies against subsequent waves of sars-cov-2 or other potentially pandemic pathogens. the number of confirmed cases of covid-19 for each brazilian municipality, up to may 22, was obtained from the ministry of health, brazil, and are publicly available at https://covid.saude.gov.br/ and at https: //brasil.io/datasets/. since the capitals of each state present different dynamics and largely concentrate covid-19 cases in the initial wave of the epidemic, we considered separately the transmission dynamics of capitals and aggregated the remaining state municipalities (which we refer throughout the text as inland cities, although strictly not all of these are distant from the shore). to evaluate state-wide enforced governmental measures, we relied upon the careful collection of government decrees and resolutions scattered throughout various state government gazettes and other official repositories, since each state uses different platforms to communicate their legislation. we annotated the type of measure enforced, the implementation date, the duration and whether it was valid to the whole state or limited to some regions. as a proxy of the population adherence to recommendations of social distancing, we used information from inloco (https://inloco.com.br/), a brazilian technology start-up that developed an index of social mobility, which seeks to help in fight the pandemic in brazil. data for the index construction is obtained from the unidentified, aggregated geo-movement patterns extracted from 60 million mobile devices throughout the country. the index ranges from 0 to 100% and measures the proportion of devices from a given municipality that remained within a 450 meter radius from the location identified as home by the device. the higher the index, the greatest the population adherence to social distancing recommendations. the data is available at https://mapabrasileirodacovid.inloco.com.br. examples of other works that used the social mobility reduction index (smri) can be found in [11, 12] . lastly, historical average daily flux data throughout the country using road/air/fluvial networks were obtained from the brazilian institute of geography and statistics [13, 14] . to comparatively evaluate the governmental measures implemented by the brazilian states, we constructed a stringency index i, similarly to that implemented in [15] . to score each employed policy we adapted the methodology to the brazilian context by taking into account the specific measures established by the different state governments. measures were classified into two categories: ordinal and cumulative. ordinal measures, denoted by o, are those in which there is a clear order on the intensity of the restriction, so that there are less possibilities of reclassification. for instance, a decree prohibiting agglomerations of more than 100 people, followed by a second decree restricting to 500 people, belong to the ordered category, where the first is more intense than the second. cumulative restrictions, denoted by c, are those with no clear order of intensity, allowing for a wide range of possibilities to classify the restriction. for instance, closure of malls and prohibition to accessing parks and beaches have no clear order to which of these measures is more intense and may lead to subjective classification. in this last case we evaluate each measure by a sum of points defined by sub-measures. the classification varies from 0 (when no measure is applied) to n i (when the most stringent measure is applied), where i corresponds to the i-th submeasure adopted. additionally, to take into account whether the measure was enforced for the whole state or limited to a particular region, each index of classification has a target g i . if the measure is ordinal, then we consider g i = go i , taking the value 0 if the measure is applied for specific areas of the state, and 1 if it is enforced for the whole state. if the measure is cumulative and since the measure will be a sum of the sub-classes, then g i = gc i is the sum of targets for each sub-class, which again is 0 if the sub-class is applied to specific areas or 1 if it is applied to the whole state without exemptions. in this work we have six classes of measures, that are described in supplementary table 1 . the summary of the six measures, as well as their sub-classes and targets are presented in table 1 . the index for the ordinal classes is given by for the cumulative measures the index is defined by where c i are sub-measures. therefore, the total state index i, for a given day, will be taken as the average of the value of the classes i i , thus yielding only measures declared by state governments were considered, given the lack of availability of centralized information regarding the municipalities, as well as the difficulty of evaluating regulations published by each of the 5,570 brazilian municipalities. federal government policies were also not considered, as these affect equally all states. . 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 june 28, 2020. . the mathematical model we generalize the usual seir model by taking into account the asymptomatic cases. to account for variations in the tr over time, we assume that the tr parameter varies according to where {t 1 , t 2 , . . . , t n } represent a set of points in time defining the change on the tr; h(t) = lim k→∞ 1 1+exp(−2kt) is the heaviside step function; and β i are trs that can be obtained by the fitting of the data to the time interval defined by the t i 's. the system of differential equations then reads: in this work we analyze the time intervals (in a daily scale) in which there were observed changes on the tr for each state, capital cities and remaining inland cities, after community transmission of the disease was declared on the state, that is when there is no clear source of origin of the infection in the community. here we estimated the β i 's, δ, p and t i 's parameters using non-linear least squares method, while κ, γ a , γ s were kept fixed. the key epidemiological model parameters and intervals were informed by the literature and are presented in supplementary table 3 . based on the obtained parameter values we also evaluated the basic reproductive number r 0 and the effective reproductive number r(t), where the first one, following the notation introduced in [9] , is expressed by: the epidemiological meaning of r(t) is the same as for r 0 , namely, it represents the average number of secondary infections that an individual, who became infected at time t, is able to generate. the series of r(t) values indicates the current trend of the epidemic and represents the dissemination of the disease in the population. as in our previous work [9] , we have: where b(t) represents the daily number of new cases and g(x) is the disease probability distribution function for the time interval between the infection of an individual and its secondary cases. the function g(x) receives contributions from the three compartments e, i a , i s that impact the evaluation of r 0 and r(t). for more details, refer to [9] . aiming at overcoming the fluctuations in the officially confirmed number of cases (which is impacted by testing capacity and its associated increase, even if momentarily, such as when pending tests accumulate over weekends), we present two series of r(t): the first, evaluated from a 7-day moving average series of the daily number of newly confirmed cases, as informed by local health authorities, while in the second r(t) series data is replaced by the predictions of the model, which effectively smooths the oscillations produced by the officially confirmed cases, since these values are given by the dynamics of the ode 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. the copyright holder for this preprint this version posted june 28, 2020. . codes used to produce the results presented herein, and related datasets, are available as supplementary material and in a public github repository [16] . this study was conducted with publicly available data from the covid-19 epidemic, published by the ministry of health of brazil or third parties. therefore, no approval by an ethics committee was required, according to resolutions 466/2012 and 510/2016 (article 1, sections iii and v) from the national health council (cns), brazil. we initially analyzed the relationship between the identification of sars-cov-2 in each state and the time interval of the declaration of community transmission by state governments, as well as the connection of virus spread and historical movement patterns of the brazilian population. in figure 2a we present the interstate flow network (road, air, fluvial), showing that states where viral spread occurred earlier, such as rio de janeiro, minas gerais, distrito federal and bahia were more likely to share a large transportation flux with the state of são paulo. on the other hand, states with the lowest interstate flows, such as acre, roraima and amapá, all located in north region, were among the last to confirm sars-cov-2 transmission. 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 this version posted june 28, 2020. . once the entry of the virus was confirmed within each state, the capitals were the most affected cities initially, emerging as the epicenter of the epidemic in each state. subsequently, sars-cov-2 disseminated throughout the inland cities with a different speed, as shown in the top panel plots of supplementary figure 1 , where the incidence of covid-19 is reported for the brazilian states. in figure 2b we show the average daily flux between all capitals and the remaining inland cities. we can see that the states of the northeast (sergipe, pernambuco, ceará, bahia), southeast (minas gerais, rio de janeiro) and south (paraná) regions present a higher historical average daily flux of people compared to the remaining states. next, we evaluated the timing of governmental interventions on the number of cases, the breadth of these interventions as measured by the stringency index, and their effects on influencing people's behavior, particularly adhesion to social distancing recommendations. . 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 june 28, 2020. . figure 2 : a) average historical daily flux of people between brazilian states through road/air/fluvial networks. state and flux colors are used only for the purpose of better identification, but otherwise have no specific meaning. b) average historical daily flux of people between state capitals (depicted as red dots) and the remaining inland cities within each state. graphs compiled using data from [13, 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 this version posted june 28, 2020. . https://doi.org/10.1101/2020.06.26.20140780 doi: medrxiv preprint a total of 547 regulations published by the 27 brazilian state governments were annotated according to the methods described to construct the stringency index. information on each individual regulation, including description, date of enforcement and validity is available in supplementary table 2 . in contrast to the pattern of disease spread observed through the states, some regions which were first affected by covid-19 were among those that delayed the implementation of measures to contain viral spread. for instance, são paulo adopted measures only 2 weeks after the confirmation of the first case, on march 13, the same day of community transmission declaration in the state. a similar scenario occurred in rio de janeiro, where the first restriction measures were only implemented in parallel to the declaration of community transmission. nevertheless, the majority of the state governments (15 out of 27) implemented restriction measures to contain the covid-19 spread on march 16, many of which weeks before declaring community transmission. indeed, six of them (to, rr, pi, pa, mt and ac) adopted measures even before the first registered case. among the measures classified in table 1 , strict quarantine measures (only adopted partially in ap, ba, ce, ma and mt) and restrictions on public transportation were the most weakly implemented measures enforced by the states. figure 3 shows the variation of the stringency index over time for each state relative to the number of confirmed cases per 100,000 inhabitants. with the exception of tocantins, mato grosso do sul, espírito santo, paraíba and piauí, all states reached stringency index values over 50% during the detection period. espírito santo and tocantins were states with the lowest values of the stringency index, ranging from 20% and 30% for an average period of 33 days, and reaching a maximum of about 40% in the remaining period. mato grosso do sul, paraíba and piauí presented stringency index values between 30% and a maximum of 45% for most of the period. the remaining states had the index varying between 50% and 75%, with ceará and amapá reaching the highest values of 84% (from may 6 to may 31) and 95% (from may 19 to may 31), respectively. however, these were the states with the highest incidence of covid-19 nationwide. variable adherence to social isolation recommendations was seen across the states, with values of the smri close to 30% at the beginning of march, followed by a peak to around 60% at the end of that month. this was observed in both state capitals and inland cities. the evolution of the stringency index for each state, as well as the smri for capitals and inland cities 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 june 28, 2020. figure 1) . our results showed that, once the smri reached its maximum, it was followed by a decreasing trend even with the maintenance of measures by state governments. with respect to the breadth and intervention period of governmental measures, our results led to the identification of three stringency index patterns: 1) increase-and-decrease (id), where the stringency index increases initially, but is followed by the lifting of measures leading to its reduction 12 . 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 june 28, 2020. . figure 4a) ; 2) increase-and-steady (is), where stringency measures reach a peak that remains constant over time (depicted by são paulo in figure 4b) ; 3) increase-and-increase (ii), where the stringency index increases successively, probably a mechanism to cope with the accelerated growth of the epidemic in some regions (illustrated by amapá in figure 4c , distributed in all regions, followed the is pattern. in addition, our results indicated that the reduction of the smri was smaller in states that followed both is and ii patterns (median reduction of -7.55% and -5.88%, respectively), compared to states that relaxed their measures according to the id pattern (median reduction of -10.71%) (figure 4d ). of note, even in states that promoted relaxation of policies, such as those that followed an id pattern, a fraction of the population close to 40% still remained in isolation (supplementary figure 1) . lastly, we sought to comparatively evaluate the effects of governmental measures and population adherence to social distancing recommendations in the tr of sars-cov-2 in the brazilian states. table 2 shows the variation of the tr obtained by the seir model, the dates when tr changes (β 0 , β 1 and β 2 parameters) occurred, and the reproduction number r 0 for each state, capital and inland cities. the majority of states presented a decrease of the tr, mainly determined by a decrease of the tr in their capitals, with the exceptions of piauí and tocantins, where capitals presented an increase of the tr. we also observed decreases in the tr throughout inland cities, with the exception of the state of acre. mato grosso do sul presenting a decrease of the tr in the capital, meanwhile the state and inland cities showed increases. three out of the 27 states (df, mt and pr), as well as the inland cities of bahia, exhibited a different behavior, in which a single change on tr (leading to β 0 , β 1 parameters) was 13 . 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 june 28, 2020. . insufficient to accurately fit the model predictions to the observed data. for these regions, we incorporated a third tr parameter over time (β 2 ), which effectively leads to two events of tr change and possibly represents an underlying feature of the dynamics of sars-cov-2 spread in these places. still in these cases, we see that all regions presented an initial decrease on the tr 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 this version posted june 28, 2020. . followed by a small increase. in 74% of the states (20/27), the changes on the tr in capital and inland cities occurred at the same time or within a 10-days window. in the remaining 36% of the states (am, ap, to, ce, ma, pi, rj), this change was only noticeable 11 days or more after tr changes in capital and inland cities. in addition, although the capitals can be considered the initial route of covid-19 spread, the results presented in table 2 reveal that the tr of inland cities is on average 10% higher than that of capitals. in the north region of brazil, on the first half of april, amapá and amazonas were the states with the highest decline of the tr and also the highest reproduction number, with decreases of 178% and 101% on the tr and r 0 values of 4.23 and 3.25, respectively. consecutively, pará and rondônia presented 37% and 62% drop in the tr on mid-april, with r 0 of 2.30 and 2.29 respectively. the remaining states (to, ac and rr) had changes on the tr occurring from may 1 to may 13 and with r 0 's between 1.6 and 2.3, with acre having the lowest variation on the tr of about 9%, mostly affected by the increase of the tr that occurred in inland cities. in the northeast region, ceará and rio grande do norte were the first to show a decrease on the tr of about 319% and 203% respectively, by the end of march. they were the states with the highest basic reproduction number compared to all states in the country, with values of 6.4 and 4.4 respectively. followed by that, on the first half of april, maranhão and bahia had 68% and 61% of decrease on the tr, with r 0 's values of 2.6 and 2.4 respectively. from april 17 to april 30, we observed decreases of the tr in the states of al, pe, pb and pi ranging from 20% to 92%, with basic reproduction numbers varying from 2.0 to 2.5. sergipe was the last state in the region to show a reduction on the rate (of around 56%) on may 13 and with r 0 of 2.1. in the midwest region, mato grosso presented the highest decrease on the tr of 83% on april 6, while mato grosso do sul presented an increase on the tr of 1.6% on april 9. df and go exhibited decreases on the transmission on the second half of april, of respectively, 31% and 27%. the reproductive number of all states in the region varied between 1.2 and 2.4, the lowest of the country. the states in south and southeast regions had changes on the tr early compared to the states of the other regions, varying between march 20 and april 14. the decrease on the tr ranged from 37% to 195%, with mg being the one with highest decrease and pr the one with the lowest reduction. the basic reproductive number varied between 2.05 in pr and 3.96 in sc. . 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 june 28, 2020. in an interactive, supplementary plot (available at https://bit.ly/ suppplotbraziltr) we present the fitting of the data to the seir model produced in this work, for both capitals and inland cities of each state. we highlight, in each plot, as vertical dashed red lines, the dates of transition from β 0 to β 1 (and β 1 to β 2 , when applicable). the blue dashed and full lines represent the evolution of the epidemic with a fixed transmission rate β 0 and with both β 0 and β 1 (where β 2 is included when suitable), respectively. the effective reproductive number is also presented for each state, capital and inland cities. the black line represents the r t calculated with reported number of new cases; the blue dashed line represents the r t calculated with the new number of simulated cases obtained from the model. the variation of the tr highlights the variations of the trends of the effective reproductive number. these results show that, in spite of the reduction of the tr in all states, in none of the regions the values of r t fell below one. in this work we evaluated the effects of non-pharmaceutical interventions and social mobility reduction patterns on the spread dynamics of sars-cov-2 throughout the 27 brazilian states, by employing an underlying seir model to estimate trs. our results show that the measures adopted, combined with the population adherence to restrict circulation, contributed to the decrease of the tr in almost all states, an effect that was perceived in both capitals and inland cities. however, in spite of the continued maintenance of governmental restrictions in most regions, population adherence to isolation recommendations gradually decreased over time, even with the expansion of cases throughout the country. this might have reflected in the r(t) values, which we observed to have decreased in all states, but still insufficiently to consider sars-cov-2 transmission controlled in the country, since it remains above 1 for all brazilian states. thus, public cooperation constitutes a particularly important challenge for tackling covid-19 in lowand middle-income countries. although the entry of the virus in brazil probably occurred as a result of multiple introductions by returning international travelers [17, 18, 19, 20] , its subsequent spread has been accelerated by the domestic transportation flows. our results point that states with historically large transportation fluxes with são paulo, initial epicenter of covid-19 in brazil, were among the first to report cases. the fact that the majority of states did not adopt measures 16 . 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 june 28, 2020. . restricting passenger transportation, or did so in a very lax manner, reinforces this observation. in addition, no brazilian state enforced strict lock-down measures as adopted by other countries. such restrictive policies have shown to significantly decrease the number of cases, deaths, and viral transmission in other countries [21, 22] . on the other hand, the economical costs imposed by harsher interventions is even more burdensome to developing countries, where large economical segments rely on consumption and services, usually involving physical contact, such as informal workers, tourism, service and retail businesses. once the entry of the virus was confirmed within each state, the capitals were the most affected initially. then, viral spread continued at different rates, with our results revealing that inland cities present increased tr compared to state capitals. this is of worry considering the large inequalities in the access to health services as well as their distribution in brazil [23, 24] , which tend to concentrate near state capitals. we also observed that downward changes on trs occurred first in the capitals, followed by the remaining cities. these results corroborate the association between population flux and viral spread [25] , and highlights the major role of state capitals to its subsequent diffusion towards smaller, inland cities. capitals also tend to centralize international airports, ports, population density and industries. accordingly, the tr observed in capitals should also affect that of inland cities, as suggested by a meta-population compartmental model [26] , but the possibility of a second-wave of covid-19 in these smaller cities, particularly with the lifting of measures, should not be ruled out. we identified common trends in the stringency index that allowed the disclosure of three patterns, with the majority of states conforming to an increase-and-steady pattern, in which the set of governmental policies adopted remained unaltered over time. states that enforced and maintained mitigation measures were likely to observe a less pronounced relaxation of stay-athome advises by their population, as measured by the smri. these results suggest the intimate relationship between the magnitude of governmental measures and the population adherence to such measures, particularly since higher values of stringency implicate in decreased opportunities of public activities. however, individuals throughout all states, in both capitals and inland cities, still reduced their adherence to social isolation in the course of time. the politicization of covid-19 in brazil [27] could have had an impact on people's behavior and compliance with sanitary recommendations, particularly when individuals downplay the health risks imposed by sars-17 . 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 june 28, 2020. . https://doi.org/10.1101/2020.06. 26.20140780 doi: medrxiv preprint cov-2, as has been suggested for a segment of the united states population [28] . we also observed that even in states that conformed to an increase-anddecrease stringency index pattern, at least a part of the population still maintained adherence to isolation. more studies are warranted to evaluate if this trend associates with specific age-groups, such as the elderly, employment status, such as individuals that have the possibility to continue working from home, education level or perception of risks around covid-19. our work has some limitations. first, in order to estimate trs (and changes thereof) we relied upon a generalized form of the seir model which explicitly considers asymptomatic transmission. thus, albeit the estimates of model parameters (or their respective search intervals) were retrieved from the literature for other countries, they could be different from the reality of the ongoing epidemic in brazil. however, while the true extent of sars-cov-2 transmission by asymptomatic and pre-symptomatic individuals is still debated, current reports conclude that it is an important route of transmission [8, 29, 30] . also, there are delays on the notification system that may be of different magnitudes throughout the regions in brazil. this limitation may impact on the perception of the implemented measures as well as compromise the planning of new ones. we used mobility data from mobile phones as proxies of social isolation as measured by the smri. in particular, the sample of devices monitored using this technology cannot be considered a representative population sample, as state/cities with superior economic status will probably exhibit increased technology adoption by their populations, leading to better accuracy of the mobility patterns in these regions. this is in contrast to rural areas, for instance, where mobile phone usage is limited [31] . however, considering the general widespread use of mobile phones in the country (with estimates that 60% of adults report owning a smartphone [32]), the general trends observed in our work should not be drastically altered by more accurate measurements of social mobility reduction. in sum, our results point to the importance of timely deployment of interventions in curbing the first-wave of the covid-19 epidemic. yet, population adherence represents a crucial factor for the success of this effort and represents a major challenge in low-and middle-income 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 this version posted june 28, 2020. table 3 . key epidemiological parameters used in the seir model, with their respective value (when fixed) or the search intervals used for parameter estimations. supplementary figure 1 . covid-19 incidence per state, their capitals and remaining inland cities (upper plots). the bottom subplots exhibit the social mobility reduction index, considered separately for capitals, inland cities and the whole state, and the stringency index, for the state measures, over time. . 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 june 28, 2020. . https://doi.org/10.1101/2020.06.26.20140780 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 this version posted june 28, 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. (which was not certified by peer review) the copyright holder for this preprint this version posted june 28, 2020. . https://doi.org/10.1101/2020.06.26.20140780 doi: medrxiv preprint who director-general's opening remarks at the media briefing on covid-19-11 ministério da saúde declara transmissão comunitária nacional social distancing measures to control the covid-19 pandemic: potential impacts and challenges in brazil an seir infectious disease model with testing and conditional quarantine the effect of control strategies to reduce social mixing on outcomes of the covid-19 epidemic in wuhan, china: a modelling study. the lancet public health first-wave covid-19 transmissibility and severity in china outside hubei after control measures, and second-wave scenario planning: a modelling impact assessment. the lancet modeling shield immunity to reduce covid-19 epidemic spread substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov-2) evaluating the burden of covid-19 on hospital resources in bahia, brazil: a modelling-based analysis of 14.8 million individuals. medrxiv modeling infectious diseases in humans and animals potential dissemination of epidemics based on brazilian mobile geolocation data. part i: population dynamics and future spreading of infection in the states of sao paulo and rio de janeiro during the pandemic of covid-19. medrxiv more than words: leaders' speech and risky behavior during a pandemic. available at ssrn 3582908 isbn: 9788524044175. ligações rodoviárias e hidroviárias isbn: 9788524042867. ligações aéreas. ibge oxford covid-19 government response tracker rede covida modelling task-force. mathematical and statistical modeling of covid-19 in brazil importation and early local transmission of covid-19 in brazil the ongoing covid-19 epidemic in minas gerais, brazil: insights from epidemiological data and sars-cov-2 whole genome sequencing evolution and epidemic spread of sars-cov-2 in brazil phylogenetic network analysis of sars-cov-2 genomes evaluation of the lockdowns for the sars-cov-2 epidemic in italy and spain after one month follow up the efficacy of lockdown against covid-19: a cross-country panel analysis. applied health economics and health policy desigualdades geográficas e sociais no acesso aos serviços de saúde no brasil inequities in access to health care in different health systems: a study in municipalities of central colombia and northeastern brazil impact of population movement on the spread of 2019-ncov in china metapopulation modeling of covid-19 advancing into the countryside: an analysis of mitigation strategies for brazil covid-19 in brazil:"so what politicizing the covid-19 pandemic: ideological differences in adherence to social distancing temporal dynamics in viral shedding and transmissibility of covid-19 estimation of the asymptomatic ratio of novel coronavirus infections (covid-19) this study was financed in part by the coordenação de aperfeiçoamento de pessoal de nível superior -brazil (capes) -finance code 001. strp was supported by an international cooperation grant (process number key: cord-347830-4rlcozy4 authors: de castro, larissa alves; lizi, jaqueline miranda; chagas, eduardo galvão leite das; de carvalho, rosemary aparecida; vanin, fernanda maria title: from orange juice by-product in the food industry to a functional ingredient: application in the circular economy date: 2020-05-06 journal: foods doi: 10.3390/foods9050593 sha: doc_id: 347830 cord_uid: 4rlcozy4 in the orange juice industry, more than 50% of raw material becomes by-products that are rich in active compounds and have high nutritional content. improved use of these by-products could represent a key strategy for a circular economy. the objective of this study was to produce a flour from orange juice by-product, characterize it, and then apply this flour to produce cookies. orange by-product flour (obpf) was characterized in terms of its chemical composition, dietary fiber, phenolic compounds, antioxidant potential, and hygroscopic properties. subsequently, the effect of substituting wheat flour by obpf in cookies was evaluated. obpf presented a very high content of dietary fiber (73.61% dry matter (dm)), minerals (ash = 2.72% dm), and total phenolic compounds (534 ± 30 mg gallic acid equivalent (gae)/100 g of dm). in general, the properties of cookies were not significantly influenced by using obpf as a substitution for wheat flour. sensorial analyses showed that cookies produced with 10% obpf presented the higher scores. therefore, obpf showed interesting characteristics, suggesting its possible use in the development of fiber enriched foods such as cookies; and its production represents a key strategy for the orange juice processing industries towards the application of a circular economy in the food system. in accordance with the food and agriculture organization (fao) [1] , one-third of all food produced in the world is wasted, which represents approximately 1.3 billion tons. waste products are largely generated by food processes, such as vegetable oil extraction, starch, juice and sugars production, and animal wastes such as bones, offal and hides, and also whey protein from cheese processing. fruits and vegetables have the highest waste rates of any food, i.e., 45% [2, 3] , which in developing regions such as asia, africa, and latin america are concentrated in agriculture and processing. because of how they are processed, a significant amount of these foods is traditionally discarded. when fruit is processed, parts such as the core, peel, pips, and kernel are discarded. although these by-products still contain nutrients and bioactive compounds, they are considered a problem. due to the high-water content of these by-products, they are prone to microbial deterioration, and therefore they are commonly used for animal feed or as fertilizer, or they are disposed of in landfills or incinerated. in addition to the inefficient use of resources and high rates of food wasted in all stages of the food system, the world population has increased. therefore, the need for more sustainable practices, with reduced environmental impacts towards the application of a circular economy in sweet oranges (citrus sinensis l. osbeck) were purchased from the local supermarket (são paulo, brazil). margarine (doriana, brazil), brown sugar (siamar, brazil), refined sugar (caravelas, brazil), wheat flour (renata, brazil), and chemical leavener (dona benta, brazil) (a mix of sodium bicarbonate, monocalcium phosphate, and calcium carbonate) were also purchased locally. for the quantification of dietary fiber (df) a k-tdfr-200a kit from megazyme international (wicklow, ireland) was acquired. the reagents used were methanol (synth, são paulo, brazil), folin-ciocalteau reagent (sigma-aldrich, bellefonte, pa, usa), sodium carbonate (synth, são paulo, brazil), gallic acid (sigma-aldrich, bellefonte, pa, usa), ferric chloride (synth, são paulo, brazil), chloridric acid (ls chemicals, ribeirão preto, brazil), (-6-hidroxi-2,5,7,8-tetramethylchroman-2-carboxilic acid (trolox; sigma-aldrich, bellefonte, pa, usa), acetic acid (synth, são paulo, brazil), sodium acetate (synth, são paulo, brazil), sodium phosphate monobasic (synth, são paulo, brazil), sodium phosphate bibasic (synth, são paulo, brazil), 2,4,6-tripyridyl-s-triazine (tptz) (sigma-aldrich, bellefonte, pa, usa), sodium fluorescein salt (sigma-aldrich, bellefonte, pa, usa), and 2,2 -azobis (2-methylpropionamidine) dihydrochloride (aaph) (sigma-aldrich, bellefonte, pa, usa). the orange by-product flour (obpf) was produced in accordance with santana [22] with some adaptations. first, oranges were manually selected, washed, and peeled. the albedo which was obtained after juice extraction was manually triturated and washed in water for 30 min. then, the material was oven-dried (marconi, ma035/5, brazil) at 60 • c for 24 h, ground in a mill (marconi, ma340, brazil), and sieved (16 mesh). the resulting obpf was stored in a refrigerator (7 • c). the moisture content, crude protein, crude fat, and ash of the obpf were determined using the methodology defined by aacc (2000) [23] . the total dietary fiber (df) was determined according to the methodology defined by aoac (1985) [24] . the extraction for the analysis of total phenolic and antioxidant potential was performed using a hydroalcoholic solution (methanol, 80:20 v/v). the sample (1 g) was added in 100 ml of solvent and homogenized (1 min, 6000 rpm) with ultra-turrax (ika, t25 digital, germany). then, the sample was vacuum filtered (tecnal, te058, brazil), using a paper filter (whatman grade 1). the retained material was extracted again two more times, however, with only 50 ml of the solvent in each step. extractions were prepared in triplicate and stored at −22 • c. the total phenolic (tp) content of the obpf was determined in accordance with singleton et al. [25] . sample extracts (0.5 ml) were added to 2.5 ml of folin-ciocalteau reagent in tubes and allowed to stand for 4 min, and then 2 ml of sodium carbonate (7.5%) was added to the tube and homogenized using a vortex agitator (ika, vortex 1v1, germany). the tubes were incubated for 2 h (25 ± 2 • c) in the absence of light. the sample absorbance was measured in a wavelength of 740 nm using a spectrophotometer (perkinelmer, lambda 35, shelton, ct, usa). gallic acid was used as the standard and the results were expressed as mg of gallic acid equivalents (gae)/100 g of dry matter. the frap assay was performed according to methodology described by benzie and strain [26] and 2.9 ml of frap solution (acetate buffer (300 mm); 2,4,6-tripiridil-s-triazina solution (10 mm); ferric chloride (20 mm); in a ratio of 10:1:1), was homogenized with 0.1 ml of extract. the mixture was kept at 37 • c for 30 min in a thermostat bath (marconi, ma 159, brazil). sample absorbance was measured in a wavelength of 593 nm in a spectrophotometer (perkinelmer, lambda 35, usa). trolox was used as an external standard and the results were reported as µmol of trolox equivalent (te)/100 g of dry matter. • orac (oxygen radical absorbance capacity) assay the orac assay was used to determine the antioxidant potential of the obpf [27] . in a microplate, an aliquot (150 µl) of fluorescein solution (81 mm) and 25 µl of extracts were added to the cells. the microplate was incubated at 37 • c for 10 min in a spectrofluorimeter (bmg labtech, fluostaroptima, german). then, 25 µl of 2,2-azobis (2-methylpropionamidino) dihydrochloride (152 mm) was added to each cell and the determination of the decay of fluorescein was performed with 485 nm excitation wavelength and 528 nm emission performed every 1 min for 120 min. trolox was used as the external standard and the results were reported as mg of trolox equivalent (te)/100 g of dry matter. the phenolic compounds identification was performed according to hassimoto et al. [28] , using a 1260 infinitquatrary quaternary lc system (agilent technologies, santa clara, ca, usa), consisting of an autosampler and a quaternary pump coupled to a diode array detector (dad). using the poroshell 2.7 µ (100 × 3 mm) column (agilent technologies, santa clara, ca, usa) with the following parameters: 0.5 ml/min flow rate and 25 • c temperature. the following two solvents were used in the mobile phase: 0.5% formic acid in water and acetonitrile. for analysis, the solvent gradient was applied as follows: 5%-18% acetonitrile at 0-7 min, 18%-28% at 7-17 min, 90% at 17.01-20 min, 5% at 21-26 min. for detection of anthocyanins, elution was monitored at 525 nm and the other flavonoids were monitored at 270 and 370 nm. lc-qtof-ms/ms analyses were performed using a prominence liquid chromatography (shimadzu, japan) coupled with an esquires-lc ion trap mass spectrometer (bruker daltonics, billerica, ma, usa) using an ionization interface electrospray (esi) and the same solvent gradient was used in the hplc-dad, reducing the flow rate to 0.2 ml/min. a positive mode esi was used to identify anthocyanins and a negative mode was used for the other flavonoid classes. the parameters required for mass spectrometer operation were as follows: collision energy at 4500 v positive mode and 4000 v negative mode and the capillary temperature was 275 • c. in order to identify the compounds, the data obtained were compared with the retention times of commercial standards when possible, also by absorption spectrum similarity, mass spectral characteristics, and comparison of literature data. the water absorption index (wai) and the water solubility index (wsi) of the obpf were determined. for the wai, the sample (1 g) was diluted in 25 ml of distilled water, using a centrifuge tube. the tubes were shaken for 30 min and placed in a centrifuge (eppendorf, centrifuge 5430-r, hamburg, germany) at 2500 rpm for 10 min. the supernatant meal contents were placed in a petri dish and the material contained in the tube was weighed. the test was performed in triplicate. the wai calculation was based on the obpf mass ratio hydrated by the dehydrated obpf mass, obtaining the result in g water/g dry matter. for the wsi, the supernatant of wai was placed in petri dishes and oven-dried (fanem, 515, brazil) for 15 h at 105 • c. the analysis was performed in triplicate, and the result, expressed as a percentage, was calculated by the ratio of the mass of the dehydrated solid to the mass of the dehydrated flour. for the oil absorption index (oai), 4 g of the obpf and 24 ml of soybean oil were placed in 50 ml centrifuge tubes, following the methodology of sosulski et al. [29] . the tubes were shaken for 30 min, followed by centrifugation at 2500 rpm for 25 min. the supernatant was discarded, and the analysis was repeated in triplicate. to calculate the oai, the mass of the insoluble residue was divided by the initial obpf mass, and the result was obtained in g oil/g dry matter. the methodology adapted from pareyt and delcour [30] was used for the production of the cookies. control cookies were produced using 238.5 g of wheat flour, 43.5 g of margarine, 86 g of refined sugar, 86 g of brown sugar, 5 g of chemical leavener, and 41 g of water (table 1) . first, margarine and sugar were mixed for 3 min in an electric mixer (kitchenaid, stand mixer pro line 6.9 l, greenville, oh, usa). then, the water was added and mixed for two more minutes. finally, the wheat flour and chemical leavener were added and mixed for two more minutes. thereafter, the obtained dough was handled and molded using a cutter (∅ = 5 mm) for cookies of approximately 16 g. the cookies were placed in a rectangular baking dish and baked in a preheated industrial oven (klimaquip cf-20, campinas, sp, brazil) for 7 min at 165 • c. preliminary tests were performed to verify maximal levels of obpf substitution. cookies produced with obpf were produced by wheat flour substitution using the obpf at concentrations of 5%, 10%, 15%, and 20%, using the same protocol. the baked cookies were measured in relation to their diameter (d) and height (h) using a micrometer. subsequently, by dividing d by h the spread factor (sf) of the cookie was determined [31] . six cookies were taken from each recipe and measured. each recipe was made in triplicate, and therefore a total of 9 values were obtained for each formulation. cookies were first weighed using a semi-analytical balance (shimadzu, são paulo, sp, brazil) and the apparent volume determined by using a volscan profile (vsp300, stable micro systems, godalming, uk) immediately after the end of baking. the specific volume was calculated by dividing the apparent volume by the weight of sample. three cookies were taken from each recipe and tested. each recipe was made in triplicate, and therefore a total of 9 values were obtained for each formulation. a texture analyzer ta-xt2 plus (texture analyzer) (stable microsystems smd, godalming, uk) equipped with a 5 kg load cell was used to measure the hardness of the cookies. a cylinder probe with a diameter of 25 mm was used to compress cookies. the parameters of velocity were set at 1.7 mm/s for test speed, 2 mm/s for pretest, and 10 mm/s for after test. each recipe was evaluated in triplicate and at least three cookies were taken from each recipe and tested. the chroma a*, chroma b*, and brightness (l*) parameters of the cookie were evaluated using a miniscan xe (hunterlab) colorimeter with illuminant d65 (daylight) and a 30 mm diameter cell opening. the morphology of the cookies was evaluated using a scanning electron microscope (sem) (tm300, tabletop microscope hitachi, japan). the samples were first frozen using liquid nitrogen, and then freeze-dried (terroni, são carlos, brazil). finally, the samples were transferred to a microscope where images were recorded at 50×, 100× and 500× magnification and with an accelerating voltage of 15 kv. in order to obtain the local cookie dough temperature increase during baking, a calibrated thermocouple (type t, ø 1 4 0.2 mm) was placed at the dough center of the different cookies and connected to a data acquisition center (keysight, hp 34972a, malaysia) [32] . during baking, the temperature profiles of the cookies were acquired every ten seconds, and thereafter plotted versus baking time, to calculate the heating rate. then, the heating rate was used to simulate the real baking condition using the differential scanning calorimetry (dsc) (dsc 2010, ta instruments, new castle, de, usa). samples (between~10 mg) were kept at 20 • c for 2 min, then heated up to 120 • c [33] . the sensory analysis was performed by 100 untrained panelists. using a 9-point verbal hedonic scale (9 = liked extremely to 1 = disliked extremely), the cookies were evaluated in relation to color, aroma, texture, flavor, and overall acceptability. prior to performing the test, panelists signed a free and informed consent term. this study was approved by the ethics committee of the faculty of animal science and food engineering (fzea/usp) (process 87793318.9.0000.5422). the statistical analyses used sas software (version 9.2, sas, inc., são paulo, sp, brazil). differences between means were determined by the duncan's test (95% confidence interval). first, orange juice was produced, before the flour production. the orange juice yield was 44.8%, in relation to total fruit. this value is close to those reported for orange juice industries, i.e., 44.8% [19] . it is important to underline that orange juice extraction, in this study, was performed manually, at a laboratory scale, using equipment with lower capacities in relation to those used in the industries, which could contribute to a lower juice yield. the obpf calculated yield was 4.2%, in relation to total fruit. the obpf chemical composition is presented in table 2 . the values obtained for water content, protein, fat, ash, dietary fiber, and glycidic fraction were 10.38 ± 0.36 g/100 g of dry matter (dm), 5.94 ± 0.1 g/100 g (dm), 0.33 ± 0.1 g/100 g (dm), 2.72 ± 0.02 g/100 g (dm), 73.61 g/100 g (dm), and 80.63 g/100 g (dm), respectively. these results, on the one hand, are in agreement with those reported by larrea, chang, and martínez bustos [34] and o'shea et al. [16] , for extruded orange pulp and orange pomace, respectively. larrea, chang, and martínez bustos [34] and o'shea et al. [16] , for extruded orange pulp and orange pomace, respectively. on the other hand, the obpf produced in this study presented a high level of total dietary fiber, i.e., 73.61% (dm), which is higher than that reported by o'shea et al. [16] , i.e., 40.47%. a high ash value, i.e., 2.72% (dm), indicates that obpf had a high mineral content. the differences in chemical composition are mainly linked to different cultivars, growing conditions, and also to fruit maturation [10] . the total phenolic (tp) content of obpf was 534 ± 30 mg gallic acid equivalent (gae)/100 g of dm (table 2) . escobedo-avellaneda et al. [35] evaluated the tp level in a whole lyophilized orange (juice, flavedo, and albedo), and the result reported was 650 ± 90 mg gae/100 g of dry matter. although the result obtained by such authors was higher, it is important to observe that those authors used the entire fruit versus only the albedo as in the present study. furthermore, the obpf was submitted to the drying process for 24 h, which could enhance the loss of phenolic compounds. danesi et al. [36] reported a lower value (450 ± 30 mg age/100 g of dry sample) for the tp content of the same sample type (albedo) in the orange by-products, which could be related to the way the fruit was grown and the heterogeneity of the material. on the basis of a comparison with the literature, it can be observed that the value found for the obpf was higher than the values reported for flours obtained from other fruit peel. infante et al. [37] reported results of tp content for * dm, dry matter; ** gae, gallic acid equivalent; and *** te, trolox equivalent. on the other hand, the obpf produced in this study presented a high level of total dietary fiber, i.e., 73.61% (dm), which is higher than that reported by o'shea et al. [16] , i.e., 40.47%. a high ash value, i.e., 2.72% (dm), indicates that obpf had a high mineral content. the differences in chemical composition are mainly linked to different cultivars, growing conditions, and also to fruit maturation [10] . the total phenolic (tp) content of obpf was 534 ± 30 mg gallic acid equivalent (gae)/100 g of dm (table 2) . escobedo-avellaneda et al. [35] evaluated the tp level in a whole lyophilized orange (juice, flavedo, and albedo), and the result reported was 650 ± 90 mg gae/100 g of dry matter. although the result obtained by such authors was higher, it is important to observe that those authors used the entire fruit versus only the albedo as in the present study. furthermore, the obpf was submitted to the drying process for 24 h, which could enhance the loss of phenolic compounds. danesi et al. [36] reported a lower value (450 ± 30 mg age/100 g of dry sample) for the tp content of the same sample type (albedo) in the orange by-products, which could be related to the way the fruit was grown and the heterogeneity of the material. on the basis of a comparison with the literature, it can be observed that the value found for the obpf was higher than the values reported for flours obtained from other fruit peel. infante et al. [37] reported results of tp content for pineapple, mango, passion fruit, and cashew residue of 240 ± 6, 450 ± 26, 343 ± 24, and 1067 ± 10 mg gae/100 g dm, respectively. it was observed that the obpf content was similar to that reported for mango by-product and higher than that of passion fruit and pineapple. although the cashew by-product is smaller, the raw material used was processed differently, since the analysis was made using the industrial by-product, not a flour, which is brought to a higher temperature and some phenolic compounds can be degraded. tp content can be degraded or transformed by exposure to high temperatures for an extended period of time [38] . the results of antioxidant potential measured by frap and orac assays are shown in table 2 . the antioxidant potential is related to the tp content, thus, the higher the concentrations of the tp content in the flour, the higher the antioxidant potential of this flour. the values reported here for the antioxidant potential measured by the frap method for the obpf are lower than those reported for the orange by-product (albedo) for juice production without the peel (49.7 ± 0.3 µmolteq/g of dm [36] ), apple bagasse (14.4 ± 0.3 mg teq/g of dm [39] ), papaya peel (25 ± 1 µmolteq/g of dm [40] ), and blueberry by-product after extraction of the juice and anthocyanins (39.8 ± 1.1 µmolteq/g of dry weight). the values determined for the antioxidant potential by the orac method corroborate that determined by escobedo-avellaneda et al. [35] (11,953 ± 538 µmolteq/100 g of dm) in a study of phytochemicals and the antioxidant potential of several orange parts. chen et al. [41] , in a characterization study of flavonoids and its association with the antioxidant potential of orange peel extracts, determined an antioxidant potential of 1117 ± 3 µmolteq/g of dm, by orac assay. this result was higher than the results reported by this study. however, this fact can be explained by the degradation of the active compounds by exposure to high temperatures for an extended period of time [38] . in a study by chen et al. [41] , the orange by-products were dried at 120 • c for 3 h, while in the present study obpf was dried for 24 h. table 3 summarizes the identified phenolic compounds obtained from the uplc-ms-ms analyses of the orange by-product flour. some of these compounds, such as quercetin 3-o-rutinoside, have biological relevance to the metabolism of carbohydrate and lipids, and therefore could attenuate some chronic diseases, i.e., hyperglycemia, dyslipidemia, and insulin resistance. furthermore, dietary plant polyphenols and polyphenol-rich products can modulate oxidative stress, and therefore the pathways sensitive to inflammatory processes [42] . there were no studies in the literature related to the profile of phenolic compounds in flour produced from the residue of the orange juice process. thus, the results presented once again show important nutritional attributes in the material produced from the industrial by-product. the values obtained for the water absorption index (wai), the oil absorption index (oai), and the water solubility index (wsi) of the obpf were 13.28 ± 0.50 g/g (dm), 2.78 ± 0.02 g (dm), and 9.94%, respectively ( table 2) . the high level of the water absorption index observed for the obpf (table 2 ) was expected, since the obpf presented high levels of total dietary fiber and the wai was usually correlated to the quantity and type of fiber [43] . figuerola et al. [44] reported values between 1.62 and 2.26 g/g (dm) for different fiber concentrates from grapefruit, lemon, orange, and apple. according to lecumberri et al. [43] , the wai values of 4.76, 0.71, and 5.53 were described for cocoa, cellulose, and carto fiber, respectively. furthermore, a comparison of the wai for obpf (13.28 g/g), and guar gum (17.72 g/g) [45] which normally is taken as a reference, with wheat flour (1.70 g/g to1.90 g/g) [46] , emphasizes the high water absorption capacity of the obpf. in relation to oil binding capacity, the obpf presented an oai of 2.78 g/g ( table 2 ). the value observed in this study was close to those reported by figuerola et al. [44] , i.e., 1.81 g/g (dm) for "valencia" cultivar orange residues. the flour nature or thickness surface of the particles influences the oai [45] , and therefore it could be proposed that the obpf particles present a higher surface which can therefore enhance its ability to adsorb and fix oil components as compared with those of figuerola et al. [44] . the sem images of the obpf (table 2 ) under close magnification suggest the presence of fibrous structures with no starch granules. o'shea et al. [16] also observed a fibrous, laminar structure, for orange pomace by-products by sem analyses images. furthermore, they suggested that the lamellar fibrous structure of the particles could represent the insoluble cellulosic fiber, which probably originated from cell wall material. figure 1 shows photographs of the cookies formulated using different levels of wheat flour substitution with orange by-product flour (obpf.) the photos were taken in the following two ways: an image of the entire cookie from the top (figure 1(a1-e1) ) and an image of the cookie when cut in half (cross section) (figure 1(a2-e2) ). figure 1 shows photographs of the cookies formulated using different levels of wheat flour substitution with orange by-product flour (obpf.) the photos were taken in the following two ways: an image of the entire cookie from the top (figure a1-e1) and an image of the cookie when cut in half (cross section) (figure a2-e2) . the cookie images show that the cookies produced with the obpf did not show important visual differences from control cookies produced with only wheat flour ( figure 1) . furthermore, the cross-section images show qualitative differences in alveoli diameter with increased obpf concentration, i.e., smaller alveoli were observed. this aspect is better discussed in the analysis of cookie microstructure (section 3.2.2). table 4 presents the results of physical properties obtained for the different cookies produced with the obpf. in general, the higher the obpf concentration, the lower the diameter, the height, and the specific volume of the cookies. however, no significant effect was observed for the spread factor. larrea et al. [47] observed a similar effect in cookies produced with extruded orange pulp. according to these authors, the pectin content enhanced water absorption, competing for the free water of dough biscuits, and therefore reduced its expansion. data expressed as mean ± standard deviation. values followed by different letter in the same line are significantly different at 95% confidence level. * scale between 1 and 9 (9 = "liked extremely" and 1 = "disliked extremely"). the higher the obpf concentration, from 0% to 20%, the lower the specific volume of cookies, from 1.56 ml 3 ·g −1 to 1.38 ml 3 ·g −1 . kohajdová et al [48] observed the same behavior for the specific volume of biscuits produced with dietary fiber from orange and lemon. the authors explained that the interaction of fiber and gluten could reduce the capacity of dough to retain air, which could explain the decrease in specific volume. (a1) (b1) (c1) (d1) (e1) (a2) (b2) (c2) (d2) (e2) the hardness values of cookies increased significantly due to the increase of the obpf concentration. the samples with 0%, 5% and 10% obpf did not differ from each other, however, samples with 15% and 20% of obpf were significantly harder. a similar effect on biscuits with increased extruded orange pulp was reported by larrea et al. [47] this increase can be related to the hardness of the fibers in this flour, as well as the obpf, as the lower hardness is the standard control formulation. in relation to the color parameters (table 4 ), it was observed that the luminosity (l*) was significantly reduced with an increase of obpf in the cookie formulation. this effect could be expected because the obpf is darker as compared with the wheat flour (standard control formulation). in baumgartner et al [49] , the incorporation of oat bran altered the color of the cookies produced, especially causing a darker color as its percentage was increased. nevertheless, no significant differences in a* and b* values were found between control samples and samples enriched with obpf. images of the control cookies formulation showed the presence of an alveolar structure, or a pore, in the matrix. this pore could be attributed to the wheat flour and to a well-developed gluten network, as in this case, dough was constituted with only wheat flour. the higher the level of wheat flour substitution with obpf, the lower the pore size/presence. the obpf had a higher level of fiber in its composition, therefore, the increase of obpf could destabilize gluten development, and could produce a more compacted dough. compared with a study by blanco et al. [50] in which they evaluated the effect of different dietary fiber inclusion in cookie dough, and related that the oat fiber presented irregular, squamous, and heterogeneous particles, the results were similar to those observed for cookies with a higher concentration of obpf. on the basis of the dsc analyses, in general, no significant differences were observed for the endothermic parameters obtained from cookies produced by different levels of wheat flour substitution with obpf (table 5) . kulp et al. [51] reported similar results in a dsc cookie study, suggesting that starch in dough cookies remained unchanged during baking. in addition, the values of transition temperatures observed in the present study are in agreement, and very close to those reported by chevallier et al. [33] for cookies produced with different ingredients. these authors reported three thermal transition temperatures, at 94, 114 and 130 • c, and related them to starch melting. pareyt and delcour [30] stated that sugar could act simultaneously as a plasticizer, by decreasing and narrowing the gelatinization temperature range, and as an anti-plasticizer, by raising the gelatinization temperature. the authors suggested that the starch did not gelatinize because the percentage of water in the sample was probably too low for gelatinization. thus, it could be supposed that the increase of obpf had the same effect, i.e., no significant difference in the phenomes of starch transition, once the sucrose level used was the same for dough cookies. table 4 shows sensory parameters of cookies produced with obpf. the substitution of wheat flour with obpf significantly influenced all sensorial attributes. incorporation of obpf at 10% levels significantly increased color, aroma, texture, flavor and overall acceptability. there were foods 2020, 9, 593 12 of 17 no significant differences between the control cookies and those prepared with 5 g/100 g obpf. furthermore, cookies with 10% of obpf presented better scores than the control for all attributes. kohajdová et al. [48] also observed the effect of lower in overall acceptance of biscuits with concentrations of orange and lemon fibers, from a concentration higher than 10%. an adequate process was proposed for developing the orange juice by-product in the food industry, representing a strategy for industries once the orange juice by-product produced represents more than 4% of total fruit. in addition, orange juice by-product flour represents a potential approach to improve "fruit" intake and dietary fiber. moreover, its complete characterization, in terms of not only its composition, but also in relation to functional properties, before its application in real and easy to manufacture food, demonstrated the potential of the obpf in food industry. notwithstanding the exposure to high temperatures during the drying, the obpf presented high concentration of total phenolic and a high antioxidant potential. in addition, high wai values are favorable for the use of obpf in bakery products. cookies produced with obpf were well accepted by tasters. all of this is in agreement with the fao recommendations. an adequate destination of by-products from industrial fruit processing represents a sustainable and key strategy, since the fruit groups are most responsible for food waste in all supply chain stages. the strategy proposed in this paper could represent a competitiveness aspect for the orange juice industry, once significant costs related to waste treatment are lowered and, at same time, there is a high value-added by-product. in addition, the by-product recycling cycle forms part of the current sustainable development and environmental protection. author contributions: l.a.d.c. is a graduate student, and she was responsible by most f paper analyses, methodology, investigation, as well, its draft. j.m.l. is also a graduate student, and she was responsible for part of obpf production, in order to helps l.a.c., and also obpf characterization, therefore, methodology, investigation. e.g.l.d.c. is an undergraduate student and colaborates with flour analyses characterization, as for example, total phenolic content, antioxidant potential and phenolic profile. r.a.d.c. is a professor, who works with the group, so she helped to design and write the paper. f.m.v. is a professor, and she was responsible for conceptualization, methodology, investigation, resources, data curation, writing-original draft, supervision and funding acquisition. all authors have read and agreed to the published version of the manuscript. the authors declare no conflict of interest. food losses and food waste save food: global initiative on food loss and waste reduction quantification of food waste per product group along the food supply chain in the european union: a mass flow analysis citrus: world markets and trade; united states department agriculture foreign agricultural service citrus fruit processing citrus: world markets and trade physical and nutritional properties of four orange varieties citrus by-products as ruminant feeds: a review valorization of citrus by-products using microwave steam distillation (msd) ethane as an alternative solvent for supercritical extraction of orange peel oils utilisation of orange by-products-orange peel carotenoids comparison of some biochemical characteristics of different citrus fruits modelling the effects of orange pomace using response surface design for gluten-free bread baking health benefits of dietary fiber world health organization. diet, nutrition and the prevention of chronic diseases: report of a joint who/fao expert consultation estudo da aplicação de nisina para a inativação de alicyclobacillus acidoterrestris effect of air-drying temperature on physico-chemical properties of dietary fibre and antioxidant capacity of orange (citrus aurantium v. canoneta) by-products food and agriculture organization of the united nations (fao) caracterização físico-química de fibra alimentar de laranja e maracujá approved methods of the american association of cereal chemists association of official analytical chemists. total dietary fiber in foods-enzimatic-gravimetric method analysis of total phenols and other oxidation substrates and antioxidants by means of folin-ciocalteu reagent the ferric reducing ability of plasma (frap) as a measure of development and validation of an improved oxygen radical absorbance capacity assay using fluorescein as the fluorescent probe identification and characterisation of anthocyanins from wild mulberry (morus nigra l.) growing in brazil functional properties of ten legume flours the role of wheat flour constituents, sugar, and fat in low moisture cereal based products: a review on sugar-snap cookies approved methods of analysis effect of the drying rate on the complex viscosity of wheat flour dough transforming into crust and crumb during baking contribution of major ingredients during baking of biscuit dough systems effect of some operational extrusion parameters on the constituents of orange pulp phytochemicals and antioxidant activity of juice, flavedo, albedo and comminuted orange effects of industrial by-products from orange, peach palm and soybean on the quality traits and antioxidant activity of flours: a response surface approach agroindustriais de frutas tropicais influence of air drying temperature on kinetics, physicochemical properties, total phenolic content and ascorbic acid of pears a survey of irish fruit and vegetable waste and by-products as a source of polyphenolic antioxidants dietary fibre concentrates produced from papaya by-products for agroindustrial waste valorisation flavonoid composition of orange peel and its association with antioxidant and anti-inflammatory activities an overview of plant phenolic compounds and their importance in human nutrition and management of type 2 diabetes dietary fibre composition, antioxidant capacity and physico-chemical properties of a fibre-rich product from cocoa (theobroma cacao l.). food chem fibre concentrates from apple pomace and citrus peel as potential fibre sources for food enrichment relationship between physical and hydration properties of soluble and insoluble fiber of artichoke comparative studies on nutritional quality of commercial wheat flour in comparative studies on nutritional quality of commercial wheat flour in bangladesh some functional properties of extruded orange pulp and its effect on the quality of cookies application of citrus dietary fibre preparations in biscuit production functional and physical properties of cookies enriched with dephytinized oat bran incorporation of dietary fiber on the cookie dough. effects on thermal properties and water availability starch functionality in cookie systems this article is an open access article distributed under the terms and conditions of the creative commons attribution (cc by) license key: cord-312555-qytl2vqt authors: da silva, josivan soares; do nascimento, andré luiz borba; alves, rômulo romeu nóbrega; albuquerque, ulysses paulino title: use of game fauna by fulni-ô people in northeastern brazil: implications for conservation date: 2020-04-17 journal: j ethnobiol ethnomed doi: 10.1186/s13002-020-00367-3 sha: doc_id: 312555 cord_uid: qytl2vqt background: due to the influence of several factors on the hunting of game meat, we investigated how the seasonality of the environment, the abundance, and the biomass of wild animals, as well as the proximity to these resources, can affect the hunting. methods: the research was developed with the fulni-ô people in the municipality of águas belas, agreste of pernambuco, northeast of brazil. in order to do this, we applied snowball sampling to select the participants. data from potentially useful game species were obtained from lists and semi-structured interviews to register their particular kind of uses, capture periods (daytime, night, or both), preferences, and perceived abundance. the hunters who allowed their game meat captured to be weighed and identified were followed for 1 year. results: our records pointed to a vast repertoire of potentially hunting animals. however, we did not verify relationships between the abundance, seasonality, and biomass of the animals that were hunted by the fulni-ô. we observed a total of 209,866 (kg) of game meat hunted in the studied group, belonging to 23 species, distributed in three taxonomic groups, the birds being the most representative group with 59% of total reported. conclusion: such consumption by the group is well below in terms of biomass when compared to other ethnic or local groups in other regions of brazil, or in caatinga areas, characterizing an activity much more of cultural character than subsistence. also, the use of game meat among the fulni-ô seems to be actively directed to the preferred species, suggesting that in the case of an urbanized indigenous community, where other sources of income are available, the demand for game meat is lower when compared to other ethnic groups. the intensive use of animals for the supply of nutritional demands by local and traditional communities worldwide has attracted the attention of several researchers due to their effects on faunal stocks caused by overexploitation [1] . the consumption of game meat is considered the primary reason for game hunting, often occurring in developing countries with great wildlife richness, mainly in the african, asian, and south american continents [1] . in brazil, despite its legal restriction, hunting persists in different socio-cultural contexts [2] [3] [4] , being allowed in subsistence conditions [5] . however, hunting of wild animals persists to a greater or lesser extent in all brazilian biomes, being strongly associated with cultural aspects and the nutritional needs of the human groups involved [3] . concerning indigenous peoples, this relationship becomes even stronger, contributing to the subsistence of these peoples, as well as to the maintenance of their cultural identity [6] [7] [8] . it is secured to them by the brazilian constitution their rights to maintain their lands, way of life, and traditions [9] . for these peoples, scientific research in the amazon has pointed out a large number of species with hunting importance that varies with their size, taxonomic group, and utilitarian purposes [2, 4, 10] . however, considering the semi-arid region, there is still little research on the dynamics of wildlife consumption by traditional communities in the northeast region of brazil [11, 12] . the hunting of wild animals involves a series of factors that may influence the choice of individual species to the detriment of others [2, 3, 10, [13] [14] [15] . the biological characteristics of species, such as abundance and biomass, for example, may direct the preference for specific prey among the hunters providing a higher post-activity yield [10] . peres [2] observed that, in several places in the amazon region, the rural population consumes between 9.6 and 23.5, birds and mammals, representing total estimated biomass of 67.173 to 164.692 tons and a yield of 36.392 to 89.224 tons of wild meat appropriate for consumption. large animals tend to be more hunted and consequently more impacted than medium and small animals [2, 10] . likewise, it is justified that taxa such as mammals and birds may be more in demand due to their biomass and abundance, respectively [1, 16] . in addition to the factors cited, climatic seasonality can affect the frequency of visitation to hunting areas [7] and the availability of these resources in the environment. these authors observed that the rainy season is considered the most favorable to hunt, due to the greater availability of food resources for the animals, easy identification of the traces left, and reduced risks of hunters being perceived. conversely, in environments with strong climatic variations, such as the caatinga, this activity may be more frequent in periods of seasonal drought, when the use of other resources becomes scarce [17] . hunting in the caatinga plays a strong socioeconomic role. thus, the use of several vertebrate groups is an important source of protein for rural and urban communities [17] . for indigenous people living in these regions, hunting sometimes becomes a more frequent activity in relation to other activities involving animals, such as fishing, due to the drought regime [18] . in these areas, even cattle breeding and pasture areas, as well as plant crops, are strongly affected by droughts, which may make hunting a subsistence alternative [10, 12] . another factor mentioned in the literature for the selection of game species is the proximity of human settlements to hunting areas. studies indicate that this variable influences not only the species choices but also the amount of biomass acquired [11, 15] . santos et al. [19] , evaluating the effect of migration and incorporation on the medicine repertoire of the truká indigenous people in the semi-arid region, that the proximity of other available resources, may favor the incorporation of new useful species into these communities. this distancing from the urban centers is related to a decrease in the availability of domesticated meat and may increase the demand for game meat. similarly, the authors argue that the proximity of useful resources decreases the costs of the search and investments of obtaining strategies [20] . however, peres and nascimento [10] point out that these meetings in the vicinity of the settlements may favor the capture of small animals that present a higher reproductive rate in relation to large animals. for the fulni-ô people, seasonality is an important factor that marks most of the activities, which are performed by the opportunities that change between the seasons [21] . thus, this research focused on the hunting of game meat among the fulni-ô people living in the semi-arid region, being the first study carried out in an ethnic group strongly influenced by urbanization in the brazilian northeast. thus, our objective was to verify the possible influences of environmental variables and biological characteristics of the species (as perceived by the people) on hunting behavior. for this, we tested if species that are perceived as more abundant by these hunters are also more hunted. we expect that the amount of annual biomass caught (kg) of species considered more abundant will be significantly higher than that of species considered less abundant. also, we verify if the proximity to the faunal resource makes it possible to obtain it. therefore, we tested if the amount of biomass caught in the months of religious ceremony, in which the members of the group move to a settlement near the ouricuri forest, is significantly higher than in other months. we also tested whether seasonality influences the hunting of game meat in the region, and we expect that the amount of biomass (kg) is significantly higher in the dry season than in the rainy season. finally, we tested if there is a relation between the preference of game species by the hunters and the hunting of game meat. we expect that the most preferred game meat biomass will be higher than the least preferred ones. the study was carried out in the fulni-ô indigenous community, located in the municipality of águas belas (9°06′ 45′′ s and 37°07′ 15′′ w) in the state of pernambuco. the fulni-ô territory occupies 11,500 ha of the municipality of águas belas [22] , presenting a caatinga biome, with a hot and humid semi-arid climate with an annual average temperature of 24.5°c. the vertebrate fauna in the caatinga is composed of about 175 reptiles and amphibians, 510 birds, and 158 mammals. the village presents tree divisions: the main village, the xixiaclá village, and the sacred village (ouricuriused in a specific period of the year). according to information obtained from the health clinic of the village, about 3430 indigenous people live in the main village, and about 100 live in the xixiaxlá village located near the ouricuri forest. their dialect characterizes the members of the fulni-ô group, "yatê," belonging to the macro-jê language group, besides the portuguese language, and by their annual religious ceremony called "ouricuri." during the ceremony, the people migrate from september to december to a region distant from the main village, surrounded by caatinga vegetation, which forms one of the fewest native forest fragments in the region [12, 23, 24] . this religious period is a time of ethnic seclusion in another village (ouricuri village) in which the fulni-ô suspend all external activities and dedicate themselves exclusively to religious demands. the main village is located a few meters from the town of águas belas and also has urban buildings. among economic activities, campos [18] emphasizes subsistence and commercial agriculture, handicrafts, rental of land, artistic presentations, and works in institutions in the municipality and other cities. also, in their rites or cultural presentations, they use body paintings extracted from local plants and, unlike other ethnic groups, they use hats made from the straw of the ouricuri palm (syagrus coronata (becc.) becc) instead of headdresses. regarding the faunistic use among them, campos [18] pointed out that fishing in the year 2012 is the predominant activity performed in the village. however, given the climatic seasonality in the region, observations during the study period indicate that fishing activity is almost incipient, since areas that allow such activity are practically nonexistent, information that is supported locally. thus, with regard to fauna, hunting among the fulni-ô people is the most frequent activity today. it usually occurs in the vicinity of the village and involves only men [18] . however, due to the proximity to the urban center of the municipality, hunting of wild animals can be replaced by the acquisition of non-wild animal protein acquired in conventional fairs and markets. the "warriors," as the hunters are called, see in this activity an important source of obtaining resources for food and religious purposes, in addition to their by-products being used in local medicine and often used for making handicrafts. the latter contains mainly byproducts of birds such as feathers that are used to make the headdresses, arrows, and decorative articles that often refer to the white man's vision of what is "indigenous" but which are not part of aldeia's traditional repertoire [25] . also, other materials of animal origin, such as teeth, skins, and claws, have been observed in situ and are frequently used in the making of these craft artifacts. exchanges can also acquire them in cultural encounters with other ethnicities. the production of handicrafts is one of the essential activities of income generation for the fulni-ô, and many of the materials used are of plant origin, mainly the ouricuri palm (s. coronata) with which they make mats, baskets, hats, among others. the environmental conditions of the region favor the choice of areas for hunting and gathering of vegetal resources. nevertheless, many of these areas have suffered successive disturbances such as burning, deforestation, and inadequate use of the soil, which leads them to develop mechanisms that guarantee their physical and cultural existence [21] . the fulni-ô hunting may occur in groups or individually, usually depending on the chosen taxon. we observed in situ that the foraging strategies among the fulni-ô people are facilitated by utilizing motorcycles or bicycles to the selected areas. collective hunts are usually planned hours or days earlier among the hunters involved. for animals like birds, collective hunting ends up being more frequent, usually occurring at night time with the aid of lanterns to immobilize the animals and firearms, or associating the use of the firearms and the assistance of dogs in daytime hunting as well. it is also common to use techniques like fall traps that are generally employed for medium and small mammals. the first contact of our research group occurred in the year 2014 for the recognition of the study area and the presentation of proposals. this contact and the selection of the study area occurred due to a relationship already established by members of our team who researched the village in previous years [23, 26, 27] . this relationship facilitated the access and the establishment of a relationship of confidence to obtain the information from the hunters. subsequently, the project adjusted to the fulniô was presented to the leaders of the village, in the person of the shaman, representative of the cacique at the time, when the proposal and stages of the research were exposed. after the explanation of the objectives of the study, we were granted the prior consent term with the approval of the leadership and authorization of the local funai. the proposal was also approved by the human research ethics committee of the university of pernambuco (caae: 94508218.0.0000.5207), and the project is registered in the national system for genetic heritage management and associated traditional knowledge -sisgen (no. aa869dc) in compliance with the provisions of law 13,123 of 2015 and its regulations. the group of the focus of the present research was people locally recognized as hunters with a minimum age of 18 years. the identification of the participants was achieved through the application of the "snowball" technique (see description in [28] ). data from potentially useful game species were obtained from free lists and semi-structured interviews [28] , and their particular kind of uses, capture periods (daytime, night, or both), preferences, and perceived abundance were recorded. we recorded at the time of the interviews which of the animals cited by each hunter were preferred. the perceived abundance was recorded individually using the "punctuation exercise" technique [29] , in which respondents attributed values between zero and ten, "zero" being equivalent to the disappearance of the species in the region and "ten" for the cases of very abundant animals. the monitoring of the hunting of game species was carried out monthly between june 2015 and july 2016. for this purpose, five hunters were selected from the indication of a key informant, due to their experience or frequency in hunting activities, being trained to register the hunted animals in the absence of researchers. these informants resided in distinct areas of the village in order to facilitate the registration of hunting by as many hunters as possible. thus, the common name of the species, the number of animals, the period of the hunting, and their respective biomass (kg) were recorded. of the 43 hunters approached in the first stage of the survey of useful species in the region, 20 aged 18 to 56 years old, allowed the registration and measurement of their games during the period of the research. the captured animals were weighed using a portable scale (up to 50 kg). to record information about local seasonality, we use the region's rainfall record as a proxy on a 10-year time scale. for this, we consulted the online database of the website of the pernambuco and water and climate agency (apac). the identification of the animals was performed with the assistance of a specialist from the federal university of paraíba through photographs taken by the hunters or the researchers at the time of the capture of the animals. additionally, for animals that were not possible to identify by photographic record, a checklist [29] (see supplementary file 1) containing images of the possible species cited by the interviewees was created. images of animals not occurring in the region were also added to avoid possible influences on hunters' indications. this technique is commonly used mainly in cases where there are difficulties in obtaining parts of the animals after their capture and use by the hunters. scientific records on the fauna occurring in the caatinga environments were used for the elaboration of this checklist [12, 17, 30, 31] , which were later presented to the people to confirm their occurrence in the locality. the classification of species in relation to their conservation status was obtained by consulting the international union for conservation of nature (iucn) (iucnredlist.org) and the red book of brazilian endangered fauna (brazilian red list). in order to analyze if the hunting of game meat was influenced by seasonality, a simple linear regression was performed between the number of animals hunted monthly and the monthly cumulative precipitation data [32] , as well as between the total weight of the hunted animals (kg) monthly and the cumulative monthly precipitation. also, to assess whether there were dissimilarities among the number of individuals hunted per species seasonally, a similarity matrix was built using the bray-curtis index. then the permanova analysis was used to check for dissimilarities between the rainy months and dry months (considering the apac classification) [32] . finally, in order to test whether there were species that could be indicative of the dry period or the rainy season according to the number of individuals hunted, the analysis of indicator species was performed. in order to analyze if there were differences in the hunting of game meat between the period of ouricuri and the rest of the year, a t test was performed between the number of individuals hunted during the ritual and non-ritual months, as well as between the weight of individuals hunted during the ritual and those hunted in other periods. in addition, to evaluate whether there were dissimilarities between the number of individuals hunted per species between the ouricuri period and the rest of the year, a similarity matrix was built using the bray-curtis index. then the permanova analysis was applied to verify if there were dissimilarities between the months of the ritual and the other months of the year. finally, in order to determine if there were species that could be indicative of the period of ouricuri according to the number of individuals hunted, the analysis of indicator species (isa) was performed. in order to evaluate if species-perceived abundance influenced hunting, a generalized linear model (glm) was applied using the "quasipoisson" family between the number of individuals hunted during the year by species and the perceived abundance average. the "quasipoisson" family was used on the species' perceived abundance data in order to ensure greater control of the degrees of freedom. the same analysis (glm) was performed considering the total weight of the game obtained during the year by species and the average abundance perceived. finally, to check if the species cited as preferred were more hunted than the other species, the mann-whitney test was performed for independent samples between the annual number of hunted individuals and the total annual weight of preferred and non-preferred hunted individuals. all analyses were performed using the software r version 3.4.1 [33] ., in which all results whose p < 0.05 were considered significant were considered. the normality of the data was verified through the shapiro-wilk test. for the analysis of permanova, the vegan package was used [34] , and the "indicspecies" package was used for the analysis of indicator species [35] . among the 64 potentially useful animals indicated from the semi-structured interviews (supplementary file 2), 22 species were frequently hunted within the period of the present study. a total of 673 animals were hunted between the years 2015 and 2016 by the fulni-ô, representing 209,866 (kg) of game meat hunted. among the animals, 77% were hunted during the day, and birds were the taxonomic group that presented 59% of the game, with the highest rate for zenaida auriculata (des murs., 1847) (26,935 kg). mammals followed birds with 27%, among which the most hunted was galea spixii (wagler, 1831) (19,775 kg). reptiles came subsequently with 14%, and the species salvator merianae (duméril & bibron, 1839) was the most hunted within this group (79,100 kg) ( table 1) . the perceived abundance of species did not explain the number of individuals hunted per month (estimated = 0.18, standard error = 0.24, t = 0.766, p > 0.05) or hunting biomass (estimated = 0.17, standard error = 0.21, t = 0.805, p > 0.05). these results show that perceived abundance is not a factor that influences the hunting of game meat. similarly, we did not observe a significant difference (t = 1.49, p > 0.05) between the number of individuals hunted in the ouricuri rituals (x = 85, dp = 51.02) and the other months of the year (x = 38.62, dp = 50.19), and there was no difference (t = − 1.86, p > 0.05) between the biomass hunted during the ouricuri ritual (x = 22.87, dp = 6.19), and after the ritual (x = 13.58, dp = 11.07). furthermore, we did not find any variation between the periods mentioned above in relation to the number of hunted species (r 2 = 0.13, f = 1.53, p > 0.05). finally, the analysis of indicator species found that only z. auriculata is significantly associated with the dry period in the region that corresponds to the same period of the ouricuri ritual (stat = 0.96, p < 0.05), being it predominantly hunted in this period. these results show us that the migratory event related to the ouricuri ritual is not a factor that generates variation in the amount of game meat hunted. the rainfall variation during the year of observation neither explained the number of individuals hunted per month (r 2 = 0.04, f = 0.471, p > 0.05) nor the biomass (r 2 = 0.01, f = 0.126; p > 0.05). in addition, there was no seasonal variation (dry and rainy) in the number of individuals hunted per species (r 2 = 0.05, f = 0.62, p > 0.05). finally, the analysis of indicator species found that only patagioenas picazuro (temminck, 1813) is significantly associated with the rainy season (stat = 0.857, p < 0.05), and it is possibly the most hunted in this period. we found significant differences (w = 112, p < 0.001) between the number of hunted individuals belonging to species cited as preferred by the informants and the other hunted species (fig. 1) . also, there was a difference (w = 91, p < 0.05) between the biomass belonging to the species cited as preferred by the informants and the other hunted species (fig. 1) . these results allow us to infer that the species cited as preferred by the informants are also the most hunted in the community. although the low number of volunteers monitored hunters in the second stage of hunting monitoring (n = 20), we believe that these data represent the current scenario of hunting among the most active hunters that allowed the collection of such information. the results on the number of animals and taxa hunted diverge from other studies regarding the annual rate of extraction of these resources in places with high faunistic diversity, such as the amazon region [2, 10, 36] , as well as in other tropical regions such as many african countries [37] [38] [39] [40] . these differences in relation to the amazon, for example, may be directly related to the faunistic composition and its size and the nutritional demands of the region [4, 10] . even when compared to studies of wild animal consumption in the caatinga region [5, 41] , the number of animals hunted is higher than that reported for the fulni-ô, which may be indicative of a lower demand for game in relation to other communities in the northeast region [5, 12, 17, 31] . these differences in the hunting of game meat observed for the funi-ô in relation to other ethnic groups lead us to infer that hunting activity is much more focused on local cultural maintenance than a subsistence strategy. that low wild meat demand may suggest that hunters target their strategies at species whose attributes for choice include cultural aspects, such as the taste of meat or taboos. campos [18] supports our idea by suggesting that hunting for this group is a food supplement for a few residential units. the author also argues that hunting is practiced for recreational purposes, domestic breeding, and the use of non-edible animals, such as some species of birds. this recent increase in wildlife utilization by the fulni-ô caused by strong drought regimes, which consequently affects fishing activity in the region, can also be interpreted as a temporal reflection that may or may not change over time, depending on the availability of other natural resources. this characteristic change in the ways of obtaining natural resources was pointed out by francesconi et al. [42] , who argued based on their findings that hunting intensity may reflect a specific context of these communities in space and time or a cultural fusion of subsistence activities. similarly, mcnamana et al. [43] reinforce the idea that preference for game meat may not be fixed, varying according to the circumstances experienced by such hunters. the cultural attributes, such as beliefs, attitudes, and social norms, are present and were equally important together with economic motivations for the hunting of wild animals in primarily urban areas [14] . besides that, other factors that may reinforce the low dependency of the fulni-ô on game meat is the involvement of hunters in other external subsistence activities and the ease of obtaining non-wild animal protein, due to the proximity to the urban centers. fita et al. [44] point out that the decrease in hunting activity may be a result of the increase of alternative productions of consumption and income generation. this possibility of external alternatives is similarly highlighted in the study by francesconi et al. [42] , mainly among younger hunters who migrate more frequently to urban areas. this migration or the urbanization processes that local/traditional communities are subjected to, despite contributing to the well-being and providing opportunities for education and access to health, is pointed out by the authors as a factor that favors habitat fragmentation in their territories, which diminishes traditional sources of subsistence [45] . the latter author also points out that such urbanization processes can also contribute to the exclusion, invisibility, and violence of these peoples in addition to influencing the detachment from their traditional practices. these factors also imply less involvement of hunters in this activity [46] [47] [48] , which leads the indigenous people to develop these practices in their free time. these factors are suggested in the literature as potential modelers of hunting practices due to the lower cost of obtaining the animal protein. likewise, most studies report a higher frequency of hunting on mammalian species, followed by birds and reptiles [10, 46] , that we did not observe in our findings. the preference for mammals is not only due to their size or availability but also to the taste of the protein in relation to the other taxa [8, 10, 15, 41] . the most common mammal species observed in our research are mainly small animals, such as g. spixii. the high frequency of use of these animals can be considered an adjustment of the hunters to the reduction of the most sought species [20, 46] . moreover, records in the literature point out that these small animals are less susceptible to hunting because of their high reproduction rate [2] and are commonly abundant in more anthropic areas [20] . on the other hand, it is important to point out that this trend towards g. spixii may also indicate a transfer of possible pressures of use in relation to other taxa of medium and large sizes [17, 41] . this requires the hunter to increase the effort to capture more of these animals to meet their demands. in addition, the defaunation that has been occurring in the semi-arid region may also be a factor for this transfer for the use of other species [17, 41] . this targeting of small species may indeed be a reflection of the decline of preferred species in the vicinity of human settlements, inducing hunters to search for animals other than their primary choices [17, 42] . the high rate of bird reported in our study is supported by other records in the literature that indicate the taxon as one of the most sought after by local communities in the caatinga [5, 41, 47] . however, the high frequency of avifauna caught among the fulni-ô should not only be a consequence of their high abundance but also of a greater efficiency in their attainment, since much of the incursions are carried out in groups and by applying a combination of strategies that optimize the success of the activity. this higher occurrence in the capture of birds, especially z. auriculata, by members of this ethnicity, if interpreted in terms of the benefits generated after capture, reinforces the local importance of the possibility of multiple uses of these animals to the detriment of other less versatile species. this versatility of use may justify the fact that many of these birds are caught for non-food purposes, especially between march and april, the period of highest intensity in the artisanal confection in the village. these are obtained exclusively for the extraction of their by-products with the purpose of making handcrafted artifacts [21] , such as headdresses and arrows. silva et al. [25] , when analyzing the artisanal production of the fulni-ô natives, also identified several artifacts that are made aiming at the external market demand, which are more related to the white man's perception of indigenous peoples. however, the need of the market and the contact with other ethnic groups can cause the indigenous people to adjust their strategies of sale. regarding the reptiles hunted in the studied region, the high rate of capture of s. merianae among the others reported may be mainly related to the return relative to biomass. in addition, like the birds, it may be related to the better use of its byproducts for local medicine, for example. this trend has been recorded in other researches that show that this lizard species is one of the most consumed in several regions of latin america, and its lard is often used in the treatment of inflammation [49] [50] [51] [52] . regarding seasonality, the migratory event related to the ritual of ouricuri (september to december), which increases the contact of fulni-ô members with natural resources, did not show a significant variation in the composition of the fauna hunted in the region. this contradicts our expectations and other studies that observed that the proximity of foraging areas is an important factor for the increase in the use of natural resources [5, 53] . this intensification of faunal use was verified by van vliet and nasi [53] in northeast of gabon, africa, where they observed a temporal and spatial variation in the period of drought in the region during the same period of the local religious ceremony. conversely, the ceremony of the fulni-ô occurs, as already mentioned, in a longer period of drought, which is a certain way that limits the encounter with animals of other taxa and favors the encounter of species of birds, mainly migratory ones like z. auriculata. this species was pointed out by mendonça et al. [5] as one of the most hunted, which justifies the abovementioned species targeting due to their high abundance during periods of scarcity from other hunting sources. however, we cannot disregard the limitation on access to information during the reclusion period for the performance of the ouricuri religious ceremony, in which this access is allowed only to members of the ethnic group. during this period, information about hunted animals was collected only by hunters who assisted us in the research. another relevant issue among the fulni-ô is that most species were hunted during the daytime. this may also be a reflection of the very legality of the hunting activity for indigenous groups. therefore, since hunting is an integral part of these cultural reaffirmation actions, it is expected that it will be performed more frequently in shifts that pose fewer risks to hunters. this safety of daytime hunting in relation to nocturnal hunting, due to better visibility of the foraging area and the greater presence of fauna preferred by the natives, may be a determining factor in the hunting practices in the village. night hunting is reported in the literature as a more costly practice, with less prey availability [53] , which requires different strategies that are usually applied in combination and facilitate visibility reducing risks [15] . our results support previous studies carried out in the caatinga region in which was observed a higher avifauna catch rate, although the low rate of vertebrate hunting observed here can be interpreted as a strong contrast between the demand of game meat from other communities and fulni-ô ethnicity. likewise, the variables abundance, biomass, and the proximity of the resource did not present strong influences in relation to the species hunted in the region. this allows us to infer that the use of game meat in the village has a strong cultural aspect of maintenance and reaffirmation of the indigenous identity and not only of subsistence. this confrontation of the fulni-ô cultural practice also can be a response to the strong influence of urbanization and the external income opportunities that allow the use of non-traditional faunal resources in the markets near the village. this lower dependence of the resource as subsistence can be reinforced by the directing of the hunt to the species pointed out as the ones that are preferred by the hunters. thus, the data presented here help to understand the dynamics of how this cultural practice occurs in the face of environmental processes such as scarcity of resources, urbanization, and aspects that are inherent to hunters, such as preferences and strategies adopted to guarantee a satisfactory return of the hunting practice. on the other hand, it is also important to note that the cultural resistance of the fulni-ô members is also supported by the preservation of their native language, their religious ceremony, and their different relationships with natural resources. thus, ethnicity presents important contexts to be investigated by future research in relation to possible cultural adjustments due to socioenvironmental factors. therefore, we emphasize the importance of integrating not only environmental or biological variables of the target species, but also cultural and social aspects about the hunting practices of traditional communities. such understanding is also fundamental concerning to the food security of these peoples, especially in the current global scenario in which we live in a pandemic caused by the covid-19 virus, whose origin and spread may have been influenced by the cultural habit of consuming wild species. from the perspective of conservation, the information presented here helps to evaluate the natural stocks of the local fauna, emphasizing the importance of integrating these communities into the management processes through strategies that stimulate such involvement, and supports the knowledge of the practice to be transmitted to the following generations. (ppgetno -ufrpe). we also acknowledge the support of the laboratory of ecology and evolution of socioecological systems from the federal university of pernambuco (lea -ufpe), all the friends who collaborate with this material, the fulni-ô indigenous people for everything, and the funding institutions that supported the present study: capes, cnpq, and facepe. authors' contributions jss have collected the data and wrote the first draft of the paper. jss and albn performed the statistical analysis. jss, rrna, and upa conceived the study and performed data analysis. the authors read and approved the final manuscript. funding institutions that supported the present study: capes, cnpq, and facepe. the datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request. not applicable. the authors declare that they have no competing interests. received: 3 january 2020 accepted: 1 april 2020 bushmeat hunting and extinction risk to the world's mammals effects of subsistence structure in hunting on vertebrate forests community hunting strategies used in the semi-arid region of northeastern brazil the uncovered volumes of bushmeat commercialized in the amazonian trifrontier between colombia bushmeat consumption and its implications for wildlife conservation in the semi-arid region of brazil how does cultural change affect indigenous peoples' hunting activity? an empirical study among the tsimane' in the bolivian amazon sabedorias, cosmologias e estratégias de caçadores numa unidade de conservação da amazônia hunting and monitoring: communitybased research in xerente indigenous land conselho nacional de segurança alimentar e nutricional (consea) impact of game hunting by the kayapo of southeastern amazonia: implications for wildlife conservation in tropical forest indigenous reserves ethnozoology in brazil: current status and perspectives hunting, use and conservation of birds in northeast brazil hunting and wildlife use in an atlantic forest remnant of northeastern brazil cultural attitudes are stronger predictors of bushmeat consumption and preference than economic factors among urban amazonians from brazil and colombia assessment of the hunting of mammals using local ecological knowledge: an example from the brazilian semiarid region caça em assentamento rural na amazônia matogrossense game mammals of the caatinga biome os fulni-ô e suas estratégias de sobrevivência e permanência no território indígena. dissertation, programa de pós-graduação em antropologia assessing the effects of indigenous migration on zootherapeutic practices in the semiarid region of brazil landscape correlates of bushmeat consumption and hunting in a postfrontier amazonian region cultura, identidade e território no nordeste indígena: os fulni-ô. série antropologia e etnicidade memória e cultura: os fulni-ô afirmando identidade étnica. (dissertation) programa de pós-graduação desenvolvimento regional rapid ethnobotanical diagnosis of the fulni-ô indigenous lands (ne brazil): floristic survey and local conservation priorities for medical plants how can local representations of changes of the availability in natural resources assist in targeting conservation? efeito da integração ao mercado sobre o conhecimento ecológico local. (dissertation) programa de pós-graduação em botânica comparisons betewen the use of medicinal plants in indigenous and rural caatinga (dryland) communities in ne brazil. boletin latinoamericano y del caribe de plantas medicinales y aromáticas ethnobotany in intermedical spaces: the case of the fulni-ô indians (northeastern brazil). evidence-based complementary and alternative medicine methods and techniques used to collect ethnobiological data use of visual stimuli in ethnobiological research diversity, natural history, and geographic distribution of snakes in the caatinga, northeastern brazil the role of game mammals as bushmeat in the caatinga, northeast brazil available from r: a language and environment for statistical computing, r foundation for statistical computing associations between species and groups of sites: indices and statistical inference meat from the wild: extractive uses of wildlife and alternatives for sustainability evaluation of mammals hunting in indigenous and rural localities in eastern brazilian amazon empty forests, empty stomachs? bushmeat and livelihoods in the congo and amazon basins the bushmeat trade in african savannas: impacts, drivers, and possible solutions mammal depletion processes as evidenced from spatially explicit and temporal local ecological knowledge hunters and hunting across indigenous and colonist communities at the forest-agriculture interface: an ethnozoological study from the peruvian amazon characterising wildlife trade market supplydemand dynamics wildlife uses and hunting patterns in rural communities of the yucatan peninsula the indigenous experience of urbanization. state of the world's minorities and indigenous peoples wildlife hunting patterns, techniques, and profile of hunters in and around periyar tiger reserve correlates of wildlife hunting in indigenous communities in the pastaza province, ecuadorian amazonia continuity and change in hunting behaviour among contemporary indigenous peoples traditional ecological knowledge about dietary and reproductive characteristics of tupinambis merianae and hoplias malabaricus in semiarid northeastern brazil reptiles used in traditional folk medicine: conservation implications el manejo de tupinambis en argentina: historia, estado actual y perspectivas futuras the trade in medicinal animals in northeastern brazil. evidence-based complementary and alternative medicine hunting for livelihood in northeast gabon: patterns, evolution, sustainability publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations supplementary information accompanies this paper at https://doi.org/10. 1186/s13002-020-00367-3. key: cord-290385-0smnl70i authors: chan, jasper f.w.; choi, garnet k.y.; yip, cyril c.y.; cheng, vincent c.c.; yuen, kwok-yung title: zika fever and congenital zika syndrome: an unexpected emerging arboviral disease date: 2016-03-03 journal: j infect doi: 10.1016/j.jinf.2016.02.011 sha: doc_id: 290385 cord_uid: 0smnl70i unlike its mosquito-borne relatives, such as dengue, west nile, and japanese encephalitis viruses, which can cause severe human diseases, zika virus (zikv) has emerged from obscurity by its association with a suspected “congenital zika syndrome”, while causing asymptomatic or mild exanthematous febrile infections which are dengueor rubella-like in infected individuals. despite having been discovered in uganda for almost 60 years, <20 human cases were reported before 2007. the massive epidemics in the pacific islands associated with the zikv asian lineage in 2007 and 2013 were followed by explosive outbreaks in latin america in 2015. although increased mosquito breeding associated with the el niño effect superimposed on global warming is suspected, genetic changes in its rna virus genome may have led to better adaptation to mosquitoes, other animal reservoirs, and human. we reviewed the epidemiology, clinical manifestation, virology, pathogenesis, laboratory diagnosis, management, and prevention of this emerging infection. laboratory diagnosis can be confounded by cross-reactivity with other circulating flaviviruses. besides mosquito bite and transplacental transmission, the risk of other potential routes of transmission by transfusion, transplantation, sexual activity, breastfeeding, respiratory droplet, and animal bite is discussed. epidemic control requires adequate clearance of mosquito breeding grounds, personal protection against mosquito bite, and hopefully a safe and effective vaccine. globalisation and urbanisation with increasingly frequent and large-scale movements of humans, animals, and commodities by aviation and water transport has led to the spread of previously geographically-restricted microbes and vectors to distant and isolated places. 1 recent examples of emerging viruses that have spilled over to other continents from their original localities via exportation of travelrelated cases include coronaviruses (severe acute respiratory syndrome coronavirus and middle east respiratory syndrome coronavirus), influenza viruses, and ebola virus. 2e11 moreover, global warming and climate changes have redefined the geographical distributions of important vectors of arthropod-borne viruses (arboviruses), such as the aedes mosquitoes, and facilitated the global spread of these viruses. dengue virus (denv), west nile virus (wnv), and chikungunya virus (chikv), have been introduced (wnv in 1999 and chikv in 2013) and/or spread rapidly in the western hemisphere in the past two decades. 12 zika virus (zikv) is an arbovirus that was little known before it caused a large outbreak on yap island of the federated states of micronesia in 2007. 13 even then, zikv was not considered as an important emerging pathogen because clinical disease was generally mild. the recent report of a possible association between zikv infection and an epidemic of microcephaly among neonates in brazil has attracted global attention. 14 the rapid spread of zikv beyond africa and asia to the americas and europe, and the potentially novel "congenital zika syndrome" outbreak have led the world health organisation (who) to declare the zikv epidemic as a global public health emergency on 1 february 2016. 15 it would therefore be important to review the current knowledge on the epidemiology, virology, clinical manifestations, and laboratory diagnosis of zikv infection, and most importantly, to formulate clinical management options with special reference to perinatal care and control measures based on comparisons made with other mosquito-borne arboviruses. important historical and epidemiological events zikv (strain mr 766) was first isolated from the blood of a febrile sentinel rhesus monkey (macaca mulatta), rhesus 766, during a study on yellow fever virus (yfv) in zika forest of uganda in april 1947 (table 1) . 16 in 1948, zikv was isolated from aedes africanus mosquitoes caught in zika forest, suggesting that the virus might be mosquito-borne. in 1954, zikv was isolated from the serum of a 10-year-old nigerian girl who had fever and headache, implying its role as a possible human pathogen. 17 further virological and/or serological evidence of human zikv infection was reported in african (uganda, tanzania, egypt, central african republic, sierra leone, and gabon) and asian (india, malaysia, the philippines, thailand, vietnam, and indonesia) countries. 18e26 zikv infection remained relatively restricted geographically with less than 20 sporadic cases reported in these areas in the first 60 years after its discovery. 13, 27 in 2007, zikv emerged outside africa and asia for the first time and caused a major outbreak on yap island of the federated state of micronesia. 13 over 70% of the yap residents who were !3 years were infected within 4 months. 13 the attack rate of zikv infection in this outbreak was 14.6 per 1000 residents (range, 3.5e21.5 per 1000 residents). subsequently, another major outbreak was reported in french polynesia in october 2013. an estimated 30,000 humans (>11% of the french polynesian population) were infected by zikv. zikv infection then spread from french polynesia to other pacific islands including new caledonia, cook islands, vanuatu, and solomon islands. 27e30 the first cases of human zikv infection in the western hemisphere occurred on easter island, chile, in february 2014, possibly originating from french polynesia during the annual tapati festival. 31 phylogenetic analysis revealed that the ns5 gene sequence of the chilean strains had !99.8% nucleotide and 100% amino acid identity to the french polynesian strains. 31 the epidemic continued to expand rapidly and autochthonous human cases were reported in many latin american countries in the ensuing 2 years. 32 brazil stands out as the hardest hit latin american country with an estimated 500,000e1,500,000 cases of zikv infection since march 2015. 33 based on the close phylogenetic relationship between the south american strains and asian and oceanic strains of zikv, the virus might have been introduced into brazil by asian travellers during the world cup or participants from the oceanic countries of the va'a world sprint championship canoe race in the summer of 2014. 30,34e36 the climate changes associated with el niño in north and eastern south america in 2015 on the background trend of global warming might have facilitated the rapid spread of aedes mosquitoes and zikv. 37 currently, >30 countries in africa, asia, south america, oceania, and micronesia have reported autochthonous cases of human zikv infection. 38 travel-related cases from endemic and epidemic regions were also reported in europe, north america, australia, and japan. 39e50 more worryingly, the brazil health ministry reported the detection of an unusual increase in the number of cases of neonates with microcephaly in northeastern brazil in october 2015, coinciding with the expanding zikv infection epidemic. 14 over 3000 suspected cases including some fatal cases were reported during the second half of 2015 alone. 14 this represented a >20-fold increase in the rate of microcephaly as compared to previous years. 32 on 24 november 2015, the french polynesia health authorities also reported an unusual increase in the number of foetal and neonatal central nervous system malformations in 2014 and 2015. 51 like other flaviviruses, zikv is mainly transmitted by mosquitoes. in addition to the sylvatic (enzootic) transmission cycle between the haematophagous mosquito vectors and susceptible primary vertebrate hosts, the recent large-scale epidemics suggest that zikv is also adapting to an urban transmission cycle. 52, 53 among the various mosquito species, aedes (stegomyia) mosquitoes appear to be the most important vector for zikv transmission, although some anopheles, culex, eretmapodites, and mansonia species have also been proposed as possible vectors (table 2) . 25,52,54e69 the animal reservoirs of zikv are unclear. non-human primates including m. mulatta, cercopithecus aethiops, c. ascanius schmidti, c. mona denti, c. albigena johnstoni, chlorocebus sabaeus, colobus abyssinicus, erythrocebus patas, and pongo pygmaeus, and other mammals including zebras, elephants, and rodents, have been suggested as possible vertebrate hosts of zikv in africa and asia, based on virological and/or serological evidence of infection. 16,54,65,68,70e72 ae. africanus is the first mosquito species from which zikv was isolated, and is likely an important vector in the sylvatic transmission cycle of zikv. 16, 54 inoculation of unfiltered supernatant of zikv-infected ae. africanus into mice and rhesus macaques led to clinical disease and/or neutralising antibody response. 16, 54 ae. hensilli is the most commonly found mosquito species on yap island, but no virus isolate was made from field-collected mosquitoes to ascertain its role as a vector for zikv transmission during the outbreak. 67 ae. aegypti and ae. albopictus, which have much wider geographical distributions than other aedes mosquitoes, are considered to be more important vectors in the urban transmission cycle of zikv. 73 these aedes mosquitoes are highly susceptible to zikv infection in vitro with potential for further transmission after an extrinsic incubation period of 5e10 days. 58, 63 they bite both indoors and outdoors, and mostly during daytime. 74 non-vector-borne transmission routes of zikv have been proposed (table 3) . like other arboviruses, blood transfusion-related transmission of zikv is possible, especially in endemic regions or where blood products obtained from infected travellers immediately returning from endemic regions are used. zikv rna was detected in the blood of 2.8% of the donors in french polynesia during the epidemic. 75 sexual transmission of zikv appears highly probable, especially in patients presenting with haematospermia with infectious viral particles and rna in semen. 76, 77 notably, no other arboviruses have been associated with haematospermia or isolated from human semen. 76 this might further complicate the control of the zikv epidemic, since most infected patients are asymptomatic. inadvertent sexual transmission of zikv to the female partner may then lead to virus transmission to the foetus, which may be potentially associated with severe congenital anomalies. besides transplacental transmission, perinatal transmission of zikv may also occur during delivery, via breastfeeding, and/or close contact after birth via exchange of saliva and other bodily fluids. zikv rna could be detected in breast milk and saliva of infected women, although replicative virus particles have not been demonstrated 78, 79 perinatal transmission of other arboviruses, including denv, chikv, wnv, and yfv, has also been reported. 80e90 other suspected routes of transmission of zivk infection are those reported for other flaviviruses. these include mucocutaneous exposure to the virus in infected blood or via monkey bite, haemodialysis, or organ transplantation. 91e96 particularly, as zikv may be shed in the urine of infected patients for more than 30 days, the risk to recipients of donated kidneys from donors at or returning from endemic areas has to be considered. 40, 41, 49, 50, 97 it is unknown whether zikv could be transmitted via respiratory droplets as viral rna could occasionally be detected in nasopharyngeal swab and saliva samples. 40, 78, 79, 96 virology and pathogenesis zikv is an enveloped, positive-sense, single-stranded rna virus belonging to the genus flavivirus in the family flaviviridae. it is closely related to spondweni virus and the 2 viruses represent the only members of their clade within the mosquito-borne cluster of flaviviruses ( fig. 1) . 98, 99 phylogenetic analysis suggests that zikv has likely emerged between 1892 and 1943 in uganda. 66 the two major lineages of zikv are the african (subdivided into west and east african) and asian lineages, which are responsible for causing the majority of infections in africa and asia (as well as the pacific and americas), respectively. 34, 69, 100 the single-stranded rna genome of zikv has a size of 10,794 nucleotides encoding 3419 amino acids, with 2 flanking untranslated regions (5 0 and 3 0 utrs) and a single long open reading frame encoding a polyprotein, which is cleaved into capsid (c), precursor of membrane (prm), envelope (e), and 7 non-structural (ns) proteins 66, 101 reverse transcription-polymerase chain reaction (rt-pcr) using primers targeting the e or ns5 gene is a key laboratory diagnostic tool for zikv infection in the recent outbreaks. 13, 102, 103 the e protein is a major virion surface protein that is involved in receptor binding and membrane fusion. the domain iii of e protein contains a panel of antigenic epitopes that are important targets of serological assays, neutralising antibodies, and vaccines. 104, 105 loss of the n154 glycosylation site in the e protein may be associated with adaptation to mosquito vectors and thus facilitate transmission. 66 a single amino acid mutation in the e protein (e1-a226v) of chikv has been reported to be associated with increased fitness of the virus in ae. albopictus and allows chikv to disseminate in regions lacking the typical ae. aegypti vector. 106 the recent spread of the asian lineage of zikv to oceania and the americas may be associated with significant ns1 codon usage adaptation to human housekeeping genes, which could facilitate viral replication and increase viral titres. 107 mutations in the e and ns1 genes should be detected in zikv strains causing the current epidemic. when an infected aedes mosquito bites an infected patient, it ingests a blood meal containing zikv. as in other flaviviruses, zikv likely replicates in the midgut epithelial cells and subsequently the salivary gland cells. after an extrinsic incubation period of 5e10 days, zikv can be found in the mosquito's saliva which can then infect human. 58, 63 moreover, the virus can likely be vertically transmitted transovarially as other flaviviruses. when the mosquito's saliva containing zikv is inoculated into human skin, the virus can infect epidermal keratinocytes, skin fibroblasts in the subcutaneous layer, and the langerhans cells. 108 the keratinocytes and fibroblasts contain axl, tyro3, and tim-1, which can serve as attachment factors or receptors for zikv. the langerhans cells contain dc-sign, which can also serve as a receptor for virus entry. 108 zikv infection of primary skin fibroblasts is associated with the upregulation with tlr3 mrna expression, and enhanced transcription of rig-i and mda5, which are known innate immune responses to rna virus infection. this is followed by enhanced expression of interferon-alpha and -beta, and their downstream pathways of immune activation. both types i and ii interferons can suppress the viral load of infected cells. moreover, zikv is capable of increasing its replication by the induction of autophagy in host cells. thus, autophagy inhibitors can decrease the viral load of infected cells. 109 infected cells of human skin explant exhibits cytoplasmic vacuolation, pyknotic nuclei, and oedema in the stratum granulosum. 108 after replication in endemic/epidemic areas: + universal nucleic acid testing of blood donors. + temporary discontinuation of blood donation (importation of blood products from blood blank centres in non-endemic regions). non-endemic/epidemic areas: + pre-donation questionnaire to identify donors with recent travel history to endemic/epidemic areas. + deferral of blood donors who have travelled to endemic areas within the preceding !14 days. + self-reporting of symptoms after blood donation ( these local tissue cells and the regional lymph nodes, zikv may then disseminate from the lymphatics and bloodstream to reach other organs/tissues, including the central nervous system, the skeletal muscles, myocardium, and perhaps transplacentally to the foetus. zikv was highly neurotropic in infected suckling mice. the brains of infected suckling mice show neuronal degeneration, cellular infiltration, and softening in the brain with virus replication in astroglial cells and neurons on histopathological examination. 16, 54, 110 moreover, evidence of inflammation in skeletal muscles and myocardium has also been demonstrated in infected suckling mice. 111 axl and tyro3 are members of the tam family of receptor tyrosine kinases (rtks). they are also present in neurons and under the influence of gonadotropin releasing hormone (grh), which in turn may affect neuronal survival and migration. furthermore, flaviviruses such as yfv may persist for up to 159 days after intracerebral inoculation in rhesus macaques. 112 the neurotropism and persistence of zikv may therefore partially explain microcephaly and predominantly neurological complications and foetal anomalies in this suspected entity of congenital zikv infection. most patients with zikv infection are asymptomatic. in the outbreak of zikv infection on yap island, only 18% of cases were estimated to be symptomatic. 13 the incubation period of zikv infection is unclear, but is estimated to be similar to other mosquito-borne flaviviruses (2e14 days). 76, 113 the clinical syndromes of symptomatic zikv infection can be broadly divided into zika fever and congenital infection ("congenital zika syndrome") ( table 4 ). zika fever is an acute "dengue fever-like" illness characterized by low-grade fever (37.8e38.5 c), rash, retroorbital headache, bilateral non-purulent conjunctivitis, myalgia, and arthritis/arthralgia with periarticular oedema of the small joints of hands and feet. 13 the rash in zika fever is typically described as a generalized, erythematous, maculopapular rash that spreads downward from the face to the limbs. 30 less commonly, some patients may have more prominent systemic symptoms including high-grade fever, chills, rigours, sore throat, hypotension, and cervical, submandibular, axillary, and/or inguinal lymphadenopathies. 74 digestive tract symptoms including nausea, vomiting, diarrhoea, constipation, abdominal pain, and aphthous ulcers may also be present. 13, 17, 19 patients with genitourinary symptoms including haematuria, dysuria, perineal pain, and haematospermia often have detectable viral rna or infectious virus particles in urine and/or semen. 76, 77 haematological and biochemical laboratory parameters are usually normal. however, some patients may have transient and mild leucopenia, neutropenia, lymphopenia or activated lymphocytes, monocytosis, thrombocytopaenia, and elevated serum levels of lactate dehydrogenase, aspartate aminotransferase, g-glutamyl transferase, fibrinogen, ferritin, c-reactive protein, and erythrocyte sedimentation rate during the viraemic phase. 29 associated with restoration of normal number of peripheral immune cells and normal function of antigen-presenting cells. 45 notably, the clinical manifestations of zika fever are non-specific and may mimic those seen in infectious diseases caused by other arthropod-borne pathogens, especially denv and chikv. some suggest that zika fever may be distinguished from dengue fever and chikungunya fever by more prominent oedema of the extremities, less severe headache and malaise, and milder degree of thrombocytopaenia seen in the former. 13, 115 moreover, haemorrhagic complications seen in dengue fever have not been reported in zika fever, and arthralgia in zika fever is less severe than that in chikungunya fever. 13 however, none of these features are pathognomonic and laboratory confirmation is required to exclude co-infections with these arboviruses and other causes of acute febrile illness in returned travellers from endemic regions, such as malaria. zika fever is usually self-limiting with most clinical manifestations resolving completely within 3e7 days. 13, 49, 116 no death, hospitalisation, or haemorrhagic complication was reported during the outbreak on yap island. 13 however, some patients may experience more protracted symptoms and other non-haemorrhagic complications. zika fever-related rash usually resolve within the first week, but may last for up to 14 days and may be pruritic. 13 other exanthematous diseases, such as denv, chikv, rubella virus, measles virus, parvovirus b19, adenovirus, enterovirus, and rickettsial infection, should be excluded. the median duration of arthralgia is 3.5 days, but some patients may develop persistent or recurrent arthralgia for more than a month after symptom onset, mimicking the post-infectious chronic arthritis seen in chikungunya fever and lyme disease. 13, 76 lymphadenopathies may be present for 2 weeks after symptom onset, and alternative diagnoses such as infectious mononucleosis-like syndrome, streptococcus pyogenes infection, and toxoplasmosis should be considered in refractory cases. 45 a post-infection asthenia appears to be frequent and further investigations may be necessary to determine possible association between zikv infection and chronic fatigue syndrome. 13, 117, 118 immune-thrombocytopenic purpura and cardiac complication have also been reported in a few cases. 114 jaundice was observed in patients with virological and/or serological evidence of zikv infection in eastern nigeria in the 1950s who had co-infections (malaria and microfilaraemia) and a patient with sickle cell anaemia. 17, 119 a possible association between zikv infection and severe neurological complications has been proposed during the recent epidemics in oceania and south america, during which the incidence of guillainebarré syndrome has increased by 8e20 times in french polynesia. 115,120 74/ 8750 (0.8%) patients with suspected zikv infection in the french polynesia outbreak developed neurological syndromes after presenting with a zika fever-like illness. 120 forty-two of these 74 (56.8%) patients were diagnosed with guillainebarré syndrome. 12, 51, 121 similarly, guil-lainebarré syndrome has been reported among patients with zika fever-like illness in south america. 51, 121 other neurological complications potentially linked to zikv infection include encephalitis, meningoencephalitis, myelitis, paraesthesia, vertigo, facial paralysis, and 48,76,114,115,120e122 suspected fatalities due to zikv-related guillainebarré syndrome have been reported. 123 while the neurotropism of zikv may partially explain these neurological manifestations, more details and serial studies on their cerebrospinal fluid and magnetic resonance images by case-control studies are required to ascertain their association. zika fever-related death appears to be extremely rare but a number of probable cases have been reported, especially among immunocompromised patients and neonates with suspected congenital zikv infection. 51,119,121 a small number of patients with coinfection with denv or hiv did not appear to have more severe disease. 29, 124 further studies should be conducted to identify patients who are at risk of severe disease or death. microcephaly (head circumference !2 standard deviations below the mean for sex and gestational age at birth) is the most prominent and commonly reported clinical feature of suspected congenital zika syndrome. 14, 125 besides microcephaly, neonates and foetuses with suspected congenital zikv infection also had other malformations (table 4 ). general features included low birth-weight, redundant scalp skin, anasarca, polyhydramnios, and arthrogryposis. neurological abnormalities included cerebral lesions, polymalformative syndromes, brainstem dysfunction, and absence of swallowing. 51 ophthalmological defects included cataract, asymmetrical eye sizes, intraocular calcifications, macular atrophy (well-defined macular neuroretinal atrophy and/or macular pigment mottling and foveal reflex loss), optic nerve hypoplasia, iris coloboma, and lens subluxation. 122, 126, 127 notably, other features characteristic of intrauterine infections, such as hepatosplenomegaly, rash, and chorioretinitis have not been reported. 14 ultrasonographic examination revealed cerebral atrophy, intracranial calcifications especially over the white matter of frontal lobes, caudate, lentostriatal vessels, cerebellum, or around the lateral and fourth ventricles, dysgenesis of corpus callosum, vermia, and thalami, enlarged cisterna magna, asymmetrical cerebral hemispheres, severe unilateral ventriculomegaly, displacement of the midline, and thinning of the parenchyma on the dilated side, pons and brainstem. 14,51,121,128 zikv particles and rna may be detected by electron microscopy and rt-pcr, respectively, in autopsied samples. 125 two important questions concerning congenital zikv infection remain unanswered. the first question is whether zikv is indeed the cause of microcephaly and other congenital anomalies in these patients. severe consequences have been reported for materno-foetal transmission of other arboviruses, such as dengue virus (preterm delivery, foetal death, low birth-weight, prematurity, acute foetal distress during labour), wnv (chorioretinitis and focal cerebral destruction), and chikv (encephalopathy and haemorrhagic fever). 80, 82, 86 preliminary analysis in the current epidemic of microcephaly has not yet completely excluded other infectious or environmental aetiologies. 51 moreover, there is some virological evidence to support the association between congenital zikv infection and these anomalies. zikv rna has been detected by rt-pcr in the amniotic fluid of 2 pregnant women whose foetuses had ultrasonographic evidence of microcephaly, in the blood and foetal tissues of a neonate with microcephaly and other congenital anomalies who died within the first 5 min of birth, and in the neonatal brain tissues of a few cases of full-term miscarriages and neonates with microcephaly. 14, 51, 121, 125 however, there is still no large-scale prospective cohort or caseecontrol study to demonstrate a causal link between the presence of zikv in the foetus and the congenital anomalies after exclusion of other infectious and toxic causes. some have suggested that the apparent microcephaly surge might be attributable to the intense search for cases due to the heightened awareness of a possible association with the zikv outbreak or the use of larvicide. 129 furthermore, detailed investigations for exclusion of other pathogens associated with congenital malformations have only been reported in a small number of cases. 14, 125 microcephaly is well reported in congenital cytomegalovirus, rubella virus, and varicella zoster virus infection. chorioretinitis and intracranial calcifications are common in congenital cytomegalovirus infection and toxoplasmosis, but the latter is more commonly associated with hydrocephalus. cataract and cardiac anomalies are characteristic of congenital rubella syndrome, although cataract can also be found in congenital herpes simplex virus infection. thus, the diagnosis of congenital zika syndrome would depend on the exclusion of these "torch" infections in future studies using clinical criteria, histopathological findings, and serological, molecular and conventional cell culture techniques. if zikv is eventually confirmed to be the cause of these congenital anomalies, the second key question would be whether congenital zika syndrome actually comprises a wider spectrum of varying clinical severities than that seen in the reported cases. as with other congenital infections, it is possible that the reported cases of microcephaly represent only the tip the iceberg, focussing on the more severely affected patients, and that the timing of infection is likely to be important in determining the severity and outcome of the affected foetus. early infection during the first or even second trimester may be associated with congenital anomalies or even intrauterine death. 14, 125, 130 indeed, preliminary data suggested that the greatest risk of microcephaly or congenital anomalies in the affected neonates appears to be associated with zikv infection in the first trimester of pregnancy. 51 of 35 mothers with infants born with microcephaly, 57% and 14% had a rash during the first and second trimester of pregnancy, respectively. 14 besides neurological defects, cardiac and muscular abnormalities should also be excluded, as suckling mice infected with zikv developed evidence of central nervous system infection, myositis and myocarditis. 111 some suspected cases of congenital zika syndrome developed severe arthrogryposis. 14, 51, 121, 128 it is possible that intrauterine zikv infections that occur at a later stage of the pregnancy may present differently, either with less severe manifestations, such as mental retardation, sensorineural deafness, and/or ophthalmological lesions, or as full-term miscarriages. 14 neonates with probable perinatal transmission of zikv infection appear to have mild disease and favourable outcome. 78 further investigations should be conducted to better define the spectrum of manifestations in different gestational stages of congenital zikv infection. definitive diagnosis of zikv infection requires laboratory confirmation as there are no pathognomonic clinical, biochemical, or radiological features that reliably distinguish zika fever from other arboviruses, and congenital zikv infection from other infective, toxic, or genetic causes of congenital anomalies. successful isolation of zikv in viral culture, the gold-standard of laboratory diagnosis of viral infections, mainly depends on the timing of specimen collection and viral loads in the specimens. zikv has been isolated in vero and vero e6 cells inoculated with infected patients' serum, urine, and/or semen samples (table 5) . 40, 75, 77 however, infectious virus particles were not recovered by culture in most specimens with low viral loads. a positive serum immunoglobulin (ig) m or 4-fold rise in the titre of neutralising antibodies in paired serum samples collected approximately 2 weeks apart also establishes the diagnosis of zikv infection. igm may be detected by enzyme-linked immunoassay on as early as day 3 of symptom onset and may last for over 2 months. 40, 49 igm antibodies to denv and wnv usually persist for 3 months and 5 months, respectively. 131e134 the major limitation of these serological tests is possible cross-reactivity with other flaviviruses. neutralising antibodies detected by plaque-reduction neutralisation test may be more specific than igm detection by elisa for primary zikv infection, but may also have indeterminate results for secondary infection, including patients with previous vaccination against or exposed to other flaviviruses. 13, 40, 102, 120 this is especially problematic in areas where there is cocirculation of multiple flaviviruses with the same aedes mosquito vectors. 13, 64, 102, 120 patients with primary zikv infection and past denv infection are more likely to have higher titre (usually !4-fold) of igm and/or neutralising antibodies against zikv than against denv or other flaviviruses. 13, 102 a positive serum denv ns1 antigen test without serial increase in igm or the combination of a positive igm response to denv and lack of an igg seroconversion in the convalescent-phase serum sample should prompt the clinician to investigate for another flavivirus such as zikv. moreover, co-infections with other mosquito-borne arboviruses, such as denv, chikv, wnv, and japanese encephalitis virus, are always possible and should be excluded by more extensive laboratory testing if clinically indicated. rapid and accurate diagnosis of zikv infection during the recent epidemics has mainly been achieved by the application of rt-pcr using primers that target the e or ns5 gene of zikv. 13, 102, 103, 135, 136 alternatively, rt-pcr sequencing using universal primers that target the conserved regions in the genomes, such as the ns5 gene, of multiple flaviviruses, may allow simultaneous detection of >50 different flaviviruses. 137 serum samples should be collected in the early phase of the disease, because viraemia is usually shortlived (usually 5 days, rarely up to 11 days) and may be low-level ( 10 2 copies/ml). 97, 102 alternatively, urine and semen samples may have higher viral rna loads table 5 advantages, limitations, and uses of different diagnostic tests and types of specimens for laboratory diagnosis of zikv infection. 14,40,41,49,50,75e79,96,97,102,121,125,127,137e139,153 may be useful to exclude concomitant infections in patients with persistent or atypical rash. may be useful to exclude concomitant infections in patients with persistent or atypical rash. may be useful to exclude concomitant infections in patients with persistent or recurrent arthritis. may be useful to exclude concomitant infections in patients with persistent or recurrent arthritis. may be useful to exclude concomitant infections in patients with unusually persistent or severe cytopenia. may be useful to exclude concomitant infections in patients with unusually persistent or severe cytopenia. other tissues brain, liver, spleen, and pooled visceral (kidney, lung, and heart) tissues were positive in a fatal case (an adult male with co-morbidities and immunosuppressive treatment). may be useful to exclude concomitant infections in patients with unusually severe or fatal infection. abbreviations: rt-pcr, reverse transcription-polymerase chain reaction; zikv, zika virus. (>10 6 copies/ml) than serum samples, and may be persistently positive for >30 days and !62 days after symptom onset, respectively. 97, 138 in a few cases, zikv rna has also been detected in saliva and nasopharyngeal swab samples of patients whose serum samples tested negative for zikv. these samples should therefore also be collected in suspected cases of zikv infection. 40, 78, 79, 96 collection of amniotic fluid should be considered in pregnant women with positive zikv test result or if the foetuses show ultrasonographic evidence suggestive of congenital zikv infection. 14, 102, 128 cerebrospinal fluid, placental, and/or umbilical cord tissues from neonates with suspected congenital zikv infection should be sent for virological and/or histopathological examinations to establish the diagnosis. 14,121,125 zikv rna may also be detected in organ tissues in the rare cases of suspected zikv-related deaths. 121 future studies should aim to better stratify the clinical use of these tests and to develop point-of-care tests (eg: antigen tests) that can be widely used in less developed regions without the facilities and expertise for molecular or serological tests. treatment is usually not required for patients with asymptomatic or uncomplicated zika fever. the mainstay of treatment is supportive as there are no specific anti-zikv antiviral agents. acetaminophen may be used to relieve fever and arthralgia. anti-histamines may help to control pruritus. adequate rehydration for fluid loss through sweating, vomiting, and insensible losses should be encouraged. aspirin should be avoided due to the risks of bleeding in those with thrombocytopaenia and developing reye's syndrome in children less than 12 years of age. nonsteroidal antiinflammatory drugs are also contraindicated in cases where denv and chikv infections cannot be confidently excluded in order to avoid haemorrhagic complications. potential neurological complications, especially guillainebarré syndrome, should be diagnosed promptly to allow early use of intravenous immunoglobulins and/or plasmapheresis. the risk of immune enhancement should also be considered if convalescent-phase plasma therapy with neutralising antibodies against zikv is used for treatment of severe cases. virological testing and foetal ultrasound to exclude zikv infection and foetal microcephaly or intracranial calcifications should be offered to pregnant women who develop zika fever-like symptoms during or within 2 weeks of travel to areas with zikv transmission. 139 besides collecting the appropriate specimens for virological tests, serial foetal ultrasound examinations should be performed every 3e4 weeks to monitor foetal anatomy and growth in suspected cases of congenital zikv infection. foetal ultrasound and/ or aminocentesis should also be offered to asymptomatic and seropositive pregnant women with history of travel to affected areas. after delivery, serum should be collected either from the umbilical cord or directly from the neonate within 2 days of birth for rt-pcr, igm and/ or neutralising antibodies against zikv. 140 comprehensive physical examination including measurement of the occipitofrontal circumference, length, and weight, evaluation for neurological abnormalities, dysmorphic features, hepatosplenomegaly, rash, ophthalmological lesions, and auditory defects, and laboratory testing for torch screening should be performed. 140 the affected child and the family should be managed and counselled by a multidisciplinary team consisting of paediatric neurologist, clinical geneticist or dysmorphologist, infectious disease specialist, medical social worker, and other relevant specialists. 140 long-term follow-up to monitor physical, intellectual, and functional progress of the child should be offered. 140 both vector control and personal preventive measures are important for interrupting the transmission of zikv. systematic mosquito surveillance and control programs should be established and coordinated by health authorities. 51 mass sanitation campaigns to eliminate mosquito breeding sites in household and high-risk areas such as garbage collection points, construction sites, illegal dumping grounds, and invalid car fields should be organised. mosquitoes should be removed with a radius of at least 400 m around areas with high population densities, such as schools, transport terminals, churches, and healthcare facilities. in areas where autochthonous or imported cases of zikv are detected, the use of adulticide through spraying to remove infected adult mosquitoes should be considered. residents in or travellers to affected areas should stay indoor with air conditioning, window and door screens if possible, wear long sleeves and pants, use permethrintreated clothing and gear, and use insect repellents when outdoor. 140 most environmental protection agency (epa)registered insect repellents, including n,n-diethyl-mtoluamide (deet), should be safe for pregnant and lactating women (20% deet), and children (10% deet) aged >2 months. 141 individuals returning from affected areas to non-affected regions should continue to use insect repellents for at least an additional 14 days to prevent local non-infected mosquitoes from the acquisition of virus from the asymptomatically infected returned travellers. this will serve to interrupt the mosquito-human-mosquito transmission chain. hospitalised laboratory-confirmed cases should be managed in designated wards to avoid mosquito bites. the effects of other novel mosquito-control measures, such as the wolbachia biological control approach, should be evaluated. 142 other animals such as rodents should also be investigated as potential animal reservoirs and controlled as findings indicate. non-vector-borne transmission of zikv may be prevented by specific measures (table 3) . concerning blood transfusion, universal nucleic acid testing of blood donors is recommended. the use of universal primers that can simultaneously detect multiple arboviruses such as denv and zikv should be considered. temporary discontinuation of blood donation should be considered during an outbreak situation. in non-endemic areas, pre-donation questionnaire to identify donors with recent travel history to regions with reported cases of zikv infection and deferral of blood donation from these donors until at least 14 days after returning from affected regions should be implemented. most transfusion-related transmissions of arboviruses are associated with asymptomatic infections, and symptomatic donors who were rt-pcr-positive for zikv usually developed symptoms between 3 and 10 days after blood donation. 143 newer pathogen reduction technologies for blood products should be considered. 143 similarly, donated organs, especially kidneys, from individuals with travel history to affected areas should be tested for zikv as the virus may persist in the genitourinary tract for an undetermined period. 40, 41, 49, 50, 97 barrier methods should be used to prevent sexual transmission through infected semen. male returned travellers should continue the use of condom with pregnant sex partner throughout the whole duration of pregnancy. future studies should evaluate the duration of virus shedding in semen and the infectiousness of rnapositive semen samples, in order to determine how long barrier methods should be used by men returning to nonendemic regions. some regional authorities have advised women to avoid pregnancy until the epidemic is over. 144 pregnant women or those planning for pregnancy should defer travelling to regions with reported cases of zikv infection. if such travel was unavoidable, they should strictly comply with personal protective measures to avoid mosquito bites. further studies are needed to determine the risk of zikv transmission by breast milk and saliva. other less common transmission routes, including mucocutaneous exposure to infected bodily fluid during laboratory and patient-care procedures, and bites by infected primates should be avoided with strict compliance to infection control measures. in the laboratory setting, zikv can be killed by potassium permanganate, ether, and heat (>60 c), but it is not effectively neutralised with low concentration (10%) of ethanol. 54 no zikv vaccine is available currently. because the moratorium for pregnancy may be impractical for some people, a safe and effective zikv vaccine is urgently needed. some realistic approaches include liveattenuated or killed vaccine from human cell lines (as in the case of yfv and japanese encephalitis vaccines), attenuated chimeric vaccine (denv vaccine using the yfv vaccine backbone, currently in phase iii clinical trial), dna and recombinant protein vaccine. 145 suitable animal models for evaluation of these potential vaccine candidates should be developed for zikv infection. the role of passive immunisation before and after exposure to zikv should also be assessed in future studies. the zikv epidemic has emerged as an unexpected global health emergency as the rapidly expanding zikv epidemic may turn out to be a major cause of permanent and severe disability in a generation of newborns, which would constitute a huge socioeconomic burden to the affected countries. the future of the zikv epidemic is unpredictable, but the worldwide spread of denv and chikv over the past two decades suggests that zikv has the potential to follow their paths. with more than half of the world's human population living in areas infested with aedes mosquitoes, the ongoing adaptation of zikv to an urban cycle signify the virus' pandemic potential. 36 research preparedness is urgently needed to improve mosquito-control measures, as well as to develop point-of-care laboratory diagnostics, antivirals, and vaccines which are suitable for use in pregnant women and foetuses. interspecies transmission and emergence of novel viruses: lessons from bats and birds severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection middle east respiratory syndrome coronavirus: another zoonotic betacoronavirus causing sars-like disease the emerging novel middle east respiratory syndrome coronavirus: the "knowns" and "unknowns is the discovery of the novel human betacoronavirus 2c emc/2012 (hcov-emc) the beginning of another sars-like pandemic? two years after pandemic influenza a/2009/h1n1: what have we learned? avian influenza a h5n1 virus: a continuous threat to humans from sars coronavirus to novel animal and human coronaviruses the emergence of influenza a h7n9 in human beings 16 years after influenza a h5n1: a tale of two cities emergence in china of human disease due to avian influenza a(h10n8) e cause for concern? ebola virus disease: a highly fatal infectious disease reemerging in west africa zika virus in the americas e yet another arbovirus threat zika virus outbreak on yap island, federated states of micronesia possible association between zika virus infection and microcephaly e brazil who statement on the first meeting of the international health regulations zika virus. i. isolations and serological specificity zika virus: a report on three cases of human infection during an epidemic of jaundice in nigeria serological and entomological study on yellow fever in sierra leone zika virus, a cause of fever in central java a serological survey of arboviruses in gabon serological survey for the prevalence of certain arboviruses in the human population of the south-east area of central african republic serological survey for arbovirus antibodies in the human and simian populations of the south-east of gabon surveillance of the circulation of arbovirus of medical interest in the region of eastern senegal a survey for arboviral antibodies in sera of humans and animals in lombok, republic of indonesia potential of selected senegalese aedes spp. mosquitoes (diptera: culicidae) to transmit zika virus epidemiological notes on some viruses isolated in uganda; yellow fever, rift valley fever, bwamba fever notes on zika virus e an emerging pathogen now present in the south pacific concurrent outbreaks of dengue, chikungunya and zika virus infections e an unprecedented epidemic wave of mosquito-borne viruses in the pacific co-infection with zika and dengue viruses in 2 patients zika virus transmission from french polynesia to brazil a report on the outbreak of zika virus on easter island epidemiological update e neurological syndrome, congenital anomalies, and zika virus infection anticipating the international spread of zika virus from brazil zika virus genome from the americas entry routes for zika virus in brazil after 2014 world cup: new possibilities zika virus in brazil and the danger of infestation by aedes (stegomyia) mosquitoes. rev soc bras med trop 2015. pii: s0037e86822015005003102 el niño and climate change-contributing factors in the dispersal of zika virus in the americas? zika situation report e neurological syndrome and congenital anomalies zika virus infection acquired during brief travel to indonesia first case of zika virus infection in a returning canadian traveler two cases of zika fever imported from french polynesia to japan first case of laboratory-confirmed zika virus infection imported into europe zika virus infection after travel to tahiti zika virus infection in a traveller returning to europe from brazil zika virus infections imported to italy: clinical, immunological and virological findings, and public health implications cytokine kinetics of zika virus-infected patients from acute to reconvalescent phase zika virus in an american recreational traveler acute zika virus infection after travel to malaysian borneo zika fever imported from thailand to japan, and diagnosed by pcr in the urines zika virus infection in a traveller returning from the maldives epidemiological alert e neurological syndrome, congenital malformations, and zika virus infection. implications for public health in the americas zika virus emergence in mosquitoes in southeastern senegal cross-species transmission and emergence of novel viruses from birds zika virus. ii. pathogenicity and physical properties a simple technique for infection of mosquitoes with viruses; transmission of zika virus isolation of zika virus from aedes aegypti mosquitoes in malaysia investigation surrounding a fatal case of yellow fever in cote d'ivoire in 1999 oral susceptibility of singapore aedes (stegomyia) aegypti (linnaeus) to zika virus twelve isolations of zika virus from aedes (stegomyia) africanus (theobald) taken in and above a uganda forest the occurrence of chikungunya virus in uganda. i. isolation from mosquitoes critical review of the vector status of aedes albopictus aedes albopictus, an arbovirus vector: from the darkness to the light aedes (stegomyia) albopictus (skuse): a potential vector of zika virus in singapore zika virus in gabon (central africa) e 2007: a new threat from aedes albopictus yellow fever and zika virus epizootics and enzootics in uganda molecular evolution of zika virus during its emergence in the 20(th) century aedes hensilli as a potential vector of chikungunya and zika viruses zika virus infections in nigeria: virological and seroepidemiological investigations in oyo state molecular characterization of three zika flaviviruses obtained from sylvatic mosquitoes in the central african republic a sero-epidemiological survey for certain arboviruses (togaviridae) in pakistan sylvatic transmission of arboviruses among bornean orangutans health evaluation of free-ranging and semicaptive orangutans (pongo pygmaeus pygmaeus) in sabah, malaysia a new threat looming over the mediterranean basin: emergence of viral diseases transmitted by aedes albopictus mosquitoes dengue and dengue vectors in the who european region: past, present, and scenarios for the future potential for zika virus transmission through blood transfusion demonstrated during an outbreak in french polynesia probable non-vector-borne transmission of zika virus potential sexual transmission of zika virus evidence of perinatal transmission of zika virus, french polynesia detection of zika virus in saliva dengue infection in pregnancy: prevalence, vertical transmission, and pregnancy outcome maternal dengue and pregnancy outcomes: a systematic review maternal and fetal consequences of dengue fever during pregnancy maternal and perinatal outcomes of dengue in portsudan, eastern sudan breast milk as a possible route of vertical transmission of dengue virus? chikungunya virus infection during pregnancy multidisciplinary prospective study of mother-to-child chikungunya virus infections on the island of la reunion west nile virus infection in pregnancy possible west nile virus transmission to an infant through breastfeeding e michigan perinatal transmission of yellow fever, brazil case report: probable transmission of vaccine strain of yellow fever virus to an infant via breast milk transmission of dengue virus without a mosquito vector: nosocomial mucocutaneous transmission and other routes of transmission laboratory-acquired west nile virus infections e united states the dengue and dengue hemorrhagic fever epidemic in puerto rico transmission of west nile virus from an organ donor to four transplant recipients possible dialysis-related west nile virus transmission e georgia zika virus infection in australia following a monkey bite in indonesia detection of zika virus in urine phylogeny of the genus flavivirus a multigene analysis of the phylogenetic relationships among the flaviviruses (family: flaviviridae) and the evolution of vector transmission genetic characterization of zika virus strains: geographic expansion of the asian lineage full-length sequencing and genomic characterization of bagaza, kedougou, and zika viruses genetic and serologic properties of zika virus associated with an epidemic, yap state, micronesia quantitative real-time pcr detection of zika virus and evaluation with field-caught mosquitoes molecular biology of flaviviruses moraes figueiredo lt. domain iii peptides from flavivirus envelope protein are useful antigens for serologic diagnosis and targets for immunization a single mutation in chikungunya virus affects vector specificity and epidemic potential spread of the pandemic zika virus lineage is associated with ns1 codon usage adaptation in humans biology of zika virus infection in human skin cells autophagy and viral diseases transmitted by aedes aegypti and aedes albopictus zika virus infection of the central nervous system of mice zika virus: further isolations in the zika area, and some studies on the strains isolated persistence of arboviruses and antiviral antibodies in vertebrate hosts: its occurrence and impacts incubation periods of mosquito-borne viral infections: a systematic review rapid risk assessment: zika virus infection outbreak, french polynesia current zika virus epidemiology and recent epidemics zika virus outbreak zika virus infection in man zika virus infection, cambodia fatal zika virus infection in girl with sickle cell disease, colombia. emerg infect dis zika virus infection complicated by guillain-barre syndrome e case report rapid risk assessment e zika virus epidemic in the americas: potential association with microcephaly and guillain-barré syndrome zika virus in brazil and macular atrophy in a child with microcephaly british broadcasting corporation (bbc) news. colombia links zika to rare nerve disorder deaths first detection of autochthonous zika virus transmission in a hiv-infected patient in rio de janeiro, brazil zika virus associated with microcephaly ophthalmological findings in infants with microcephaly and presumable intra-uterus zika virus infection ocular findings in infants with microcephaly associated with presumed zika virus congenital infection in salvador, brazil zika virus intrauterine infection causes fetal brain abnormality and microcephaly: tip of the iceberg? zika virus: brazil's surge in small-headed babies questioned by report viral infections during pregnancy levels of igm antibodies against dengue virus in rio de janeiro persistence of virus-reactive serum immunoglobulin m antibody in confirmed west nile virus encephalitis cases development and persistence of west nile virusspecific immunoglobulin m (igm), iga, and igg in viremic blood donors virus and antibody dynamics in acute west nile virus infection one-step rt-pcr for detection of zika virus a diagnostic polymerase chain reaction assay for zika virus universal primers that amplify rna from all three flavivirus subgroups detection of zika virus in semen interim guidelines for pregnant women during a zika virus outbreak e united states interim guidelines for the evaluation and testing of infants with possible congenital zika virus infection e united states zika virus spreads to new areas e region of the americas wolbachia and the biological control of mosquito-borne disease zika virus and the never-ending story of emerging pathogens and transfusion medicine jamaica advises women to avoid pregnancy as zika virus approaches a review of successful flavivirus vaccines and the problems with those flaviviruses for which vaccines are not yet available arthropod-borne viral infections of man in nigeria dengue and other arboviral diseases in south-east asia zika virus, french polynesia, south pacific rapid spread of emerging zika virus in the pacific area first report of autochthonous transmission of zika virus in brazil zika virus spreads across americas as concerns mount over birth defects zika virus-related hypertensive iridocyclitis laboratory infection with zika virus after vaccination against yellow fever the study was partly supported by the consultancy service for enhancing laboratory surveillance of emerging infectious disease of the department of health, the food and health bureau, hong kong special administrative region, china; and by the donations of hui hoy and chow sin lan charity fund limited and mr. larry chi-kin yung. the authors declare no conflict of interest. key: cord-257582-e9306xae authors: day, m. j.; crawford, c.; marcondes, m.; squires, r. a. title: recommendations on vaccination for latin american small animal practitioners: a report of the wsava vaccination guidelines group date: 2020-03-30 journal: j small anim pract doi: 10.1111/jsap.13125 sha: doc_id: 257582 cord_uid: e9306xae the world small animal veterinary association vaccination guidelines group has produced global guidelines for small companion animal practitioners on best practice in canine and feline vaccination. recognising that there are unique aspects of veterinary practice in certain geographical regions of the world, the vaccination guidelines group undertook a regional project in latin america between 2016 and 2019, culminating in the present document. the vaccination guidelines group gathered scientific and demographic data during visits to argentina, brazil and mexico, by discussion with national key opinion leaders, visiting veterinary practices and review of the scientific literature. a questionnaire survey was completed by 1390 veterinarians in five latin american countries and the vaccination guidelines group delivered continuing education at seven events attended by over 3500 veterinarians. the vaccination guidelines group recognised numerous challenges in latin america, for example: (1) lack of national oversight of the veterinary profession, (2) extraordinary growth in private veterinary schools of undetermined quality, (3) socioeconomic constraints on client engagement with preventive health care, (4) high regional prevalence of some key infectious diseases (e.g. feline leukaemia virus infection, canine visceral leishmaniosis), (5) almost complete lack of minimal antigen vaccine products as available in other markets, (6) relative lack of vaccine products with extended duration of immunity as available in other markets, (7) availability of vaccine products withdrawn from other markets (e.g. giardia vaccine) or unique to latin america (e.g. some leishmania vaccines), (8) accessibility of vaccines directly by pet owners or breeders such that vaccination is not delivered under veterinary supervision, (9) limited availability of continuing education in veterinary vaccinology and lack of compulsion for continuing professional development and (10) limited peer‐reviewed published scientific data on small companion animal infectious diseases (with the exception of leishmaniosis) and lack of support for such academic research. in this document, the vaccination guidelines group summarises the findings of this project and assesses in evidence‐based fashion the scientific literature pertaining to companion animal vaccine‐preventable diseases in latin america. the vaccination guidelines group makes some recommendations on undergraduate and postgraduate education and academic research. recognising that current product availability in latin america does not permit veterinarians in these countries to vaccinate according to the global world small animal veterinary association guidelines, the vaccination guidelines group makes a series of “pragmatic” recommendations as to what might be currently achievable, and a series of “aspirational” recommendations as to what might be desirable for the future. the concept of “vaccine husbandry” is addressed via some simple guidelines for the management of vaccine products in the practice. finally, the vaccination guidelines group emphasises the global trend towards delivery of vaccination as one part of an “annual health check” or “health care plan” that reviews holistically the preventive health care needs of the individual pet animal. latin american practitioners should transition towards these important new practices that are now well embedded in more developed veterinary markets. the document also includes 70 frequently asked questions and their answers; these were posed to the vaccination guidelines group during our continuing education events and small group discussions and should address many of the issues surrounding delivery of vaccination in the latin american countries. spanish and portuguese translations of this document will be made freely available from the on‐line resource pages of the vaccination guidelines group. the world small animal veterinary association (wsava) vaccination guidelines group (vgg) was established in 2004 with the remit of providing globally applicable evidence-based advice for small companion animal veterinary practitioners on best practice for vaccination of pet dogs and cats. the vgg first released global vaccination guidelines for veterinarians in 2007 and these were updated in 2010 and 2016 (day et al. 2016 ) and translated into multiple languages. the main body of the wsava vaccination guidelines are most applicable to pet cats and dogs living predominantly in and around their owners' homes (rather than living 100% outdoors or in large, closely-packed groups), but advice is also given on vaccination in a shelter setting. the 2010 and 2016 revisions were accompanied by a separate document providing information on vaccination for the owners and breeders of dogs and cats and by a series of infectious disease "fact sheets" designed to be used by veterinarians during consultation with clients (https://www.wsava. org/guidelines/vaccination-guidelines). from 2012 to 2014 the vgg worked on a regional project focussing on the vaccination requirements of small companion animals in asia (day et al. 2015 ). following from the success of that project the vgg embarked on a second regional project in latin america (latam) between 2016 and 2019. the present paper represents the final outcome from this latam project. it summarises the key challenges faced by small companion animal veterinary practitioners in latam and makes a series of recommendations for future actions that might benefit the profession, pet owners and dogs and cats in these countries. the manuscript will be made available in spanish and portuguese translation via the vgg webpages (see above). the vgg recognises that latam is a vast and diverse region comprised of numerous countries with distinctly different geography, climate, culture and socioeconomics; all of which may impact on the keeping of companion animals, the prevalence and distribution of key companion animal infectious diseases and the accessibility of veterinary preventive health care for those animal populations. the vgg could not visit every country in the region, but, as described below, gathered extensive data on which to base our comments and recommendations. we believe that the majority of these recommendations will have applicability across the latam region. the membership of the vgg was changed for the latam project. emeritus professor m. j. day and professor r. a. squires were joined by professors c. crawford and m. marcondes; the latter recruited as a regional expert in small companion animal infectious disease and vaccinology. the principle aim of the project was to gather as much information and scientific evidence concerning small companion animal practice, vaccine-preventable infectious diseases and vaccination of dogs and cats as possible, to form a firm basis for the recommendations to be made subsequently. to that end, the vgg undertook three fact-finding visits to argentina (buenos aires and rosario in 2016), brazil (são paulo and rio de janeiro in 2017) and mexico (mexico city, guadalajara and monterrey in 2018). each of these visits was similarly structured and involved formal small group discussions with key opinion leaders (kols) including (1) first opinion veterinary practitioners, (2) representatives of small animal veterinary associations, (3) academic veterinarians involved in companion animal infectious disease research and the teaching of microbiology, immunology, clinical medicine and vaccinology, (4) government officials responsible for the assessment and licensing of small companion animal vaccines and (5) representatives of national and international vaccine manufacturers and distributors. the formal meetings were supplemented with site visits to veterinary practices in each of the seven cities; these were purposely selected to show a range of sizes and standards. scientific literature relevant to the vgg mission was collected by on-line database searching and directly from academics participating in kol meetings. during 2019, the vgg met to discuss findings and draft this final report. in order to expand the information gained from these face-to-face meetings, the vgg developed a questionnaire for distribution among first opinion practitioners in the target countries (appendix). the questionnaire was designed using "google forms" (https:// www.google.com/intl/en-gb/forms/about/) and was accessed and completed on-line. the questionnaire was made available in portuguese and spanish and was completed anonymously with instruction that only one veterinarian from each practice should undertake the survey. the responses were analysed (using tools in the google survey programme) and summarised. through the survey, the vgg gathered information about (1) the demographics of the responding practitioners, (2) veterinary practices and their access to diagnostic laboratories, (3) canine and feline infectious diseases seen in the practices and (4) canine and feline vaccines and vaccination protocols used in the practices. responses to the surveys were received from 175 practitioners in argentina, 579 in brazil and there is little doubt that latam is experiencing remarkable growth in pet ownership and the associated pet care industry. a 2016 survey by gfk global of 27,000 consumers in 22 different countries revealed that latam has the highest level of global pet ownership. eighty percent of the online population surveyed in argentina and mexico, and 75% of the surveyed population of brazil, owned a pet. of the pet owners, 66% in argentina, 64% in mexico and 58% in brazil owned dogs and 32, 24 and 28%, respectively, owned cats (https://www.gfk.com/fileadmin/user_upload/country_one_pager/nl/documents/global-gfk-survey_pet-ownership_2016. pdf ). there are no accurate figures for national dog and cat populations. in 2014, there were an estimated 52.2 million dogs and 22.1 million cats in brazil (conceição 2016) and argentinian kols estimated up to 10 million dogs and 3 million cats in argentina. in some regions, many of these animals will be free roaming rather than being owned-housed pets. with such growth should come an increasing demand for veterinary services and preventive health care for companion animals, including providing protection from infectious disease for the individual animal and animal population ("herd immunity") by vaccination. the vgg discussed these demographics with academic and association colleagues in argentina, brazil and mexico. we met with academic administrators and teacher/researchers from several veterinary schools in each country. a general observation was that it appeared challenging to provide accurate and up-to-date data on the demographics of the profession in the absence of national (as opposed to provincial or state) professional regulatory authorities who might ensure the quality of veterinary education, register veterinary graduates, maintain registers of practicing veterinarians and ensure that they undertake continuing professional development. some estimates were given for the numbers of veterinarians in argentina (21,000), brazil (130,000 active veterinarians) and mexico (45, 000) . the numbers of veterinary schools were estimated at 21 in argentina and 45 in mexico and these are within a mixture of public and private universities. the most extraordinary growth in veterinary schools has occurred in brazil where a marked rise in the number of private institutions offering a veterinary curriculum means that there are currently thought to be over 400 schools in the country (brazilian federal council of veterinary medicine, personal communication). sixty-three of these are in state-or federallyfunded public universities with the remainder being in the private sector. there are no centralised national curricula and the content and standard of teaching appears to be very variable. there were wide differences in the proportions of the curricula devoted to teaching of companion animal infectious diseases, immunology and vaccinology. similarly, approaches to teaching the clinical application of vaccination in the consultation room setting were inconsistent. ce is not mandatory for veterinarians and there is no scheme for recording or recognising participation in professional development. opportunities for ce are provided through association congresses, private commercial congresses and lectures (physical and by online webinar) provided by industry. in brazil, in particular, industry has an active programme for delivering ce in vaccinology by supporting lectures on the subject. in latam, many veterinary practices are small and run by single veterinarians. this creates a challenge for those veterinarians to be able to leave their practice in order to attend ce events. many of the academic colleagues with whom the vgg met were engaged in and publishing scientific research on companion animal infectious diseases. these studies form the evidence-based scientific literature for latam and where appropriate they are referenced in this document. the global challenge of obtaining research funding for companion animal studies applies equally in latam, but because of the zoonotic significance of canine visceral leishmaniosis, this is a particularly well-investigated disease in brazil. at the practice level there are many issues with the diagnosis of companion animal infectious diseases. most practices have access to point-of-care serological infectious disease diagnostic test kits, but not to diagnostic laboratories offering alternative methodologies. there is often misunderstanding of the limitations of the test kits used and the most appropriate methods for confirming a diagnosis of infectious disease. latin america encompasses a vast land mass (over 20 million km 2 in area) comprising 20 countries and a human population of over 650 million. more importantly, when considering infectious disease frequencies, it includes parts of north, south and central america as well as some caribbean islands. it extends a vast distance from north to south, spanning the equator and including temperate, subtropical and tropical climatic zones. the region includes ecosystems ranging from desert to high mountains to tropical rain forest. it would therefore be expected that infectious disease frequencies would vary markedly from region to region within this vast, diversified area. disease frequencies in some parts of latin america have been studied thoroughly (and shown, indeed, to vary widely) while many other areas have not been studied at all. the vgg obtained information on the nature and prevalence of vaccine-preventable canine and feline infectious diseases in latam via three methods: (1) review of the peer-reviewed scientific literature, (2) by discussion with key opinion leaders in small group meetings and (3) by questionnaire survey of veterinarians as described above. the results of the questionnaire survey clearly showed that, in the five countries surveyed, the major canine vaccine-preventable infectious diseases are recognised by veterinary practitioners, in particular infections caused by canine distemper virus (cdv) (recognised by 88 to 96% of respondents), canine parvovirus type 2 (cpv2) (recognised by 88 to 94% of respondents) and leptospira spp. (recognised by 49 to 68% of respondents) ( table 1 ). the canine infectious respiratory disease complex (cirdc; "kennel cough") is also widely recognised (by 88 to 98% of respondents). although canine rabies is variably controlled in the latam countries (see below), cases are still recognised in all countries (by 6 to 12% of respondents). not surprisingly, cases of canine visceral leishmaniosis (cvl) are most often recognised in brazil (by 58% of respondents) but appear to occur also in the other four countries (recognised by 3 to 11% of respondents). the data in tables 1 and 2 are of uncertain accuracy. they represent responses from veterinarians as to whether they recognise, clinically, these diseases in their practices and do not explore how robustly these diseases might have been diagnosed or confirmed microbiologically. for the major vaccine-preventable feline infectious diseases, veterinarians in the five countries clearly reported recognising infections caused by feline parvovirus (fpv) (42 to 60% of respondents), feline herpesvirus type 1 (fhv1) (30 to 95% of respondents), feline calicivirus (fcv) (55 to 78% of respondents) and chlamydia felis (18 to 50% of respondents). there appears to be widespread recognition of feline retroviral diseases and elsewhere we describe the high prevalence of these infections in certain regions. respondents to the survey recognised feline leukaemia virus (felv) infection (63 to 97% of respondents) and feline immunodeficiency virus (fiv) infection (57 to 91% of respondents) in their practices. although a vaccine against feline infectious peritonitis (fip) is not available in most parts of the world, including latam, we also gathered data on fip infection, which was recognised by 47 to 76% of respondents. cases of rabies in cats were reported by 2 to 9% of respondents. the same qualification concerning the robustness of these data (see above) applies to the information on feline infectious diseases. a summary of the relevant latam published scientific literature on these canine and feline infectious diseases is given in the sections below. high-quality epidemiological studies evaluating the distribution of infectious diseases in latam are scarce and although there are some reports, just a few published studies defined the diseases based on clinical presentation with confirmatory laboratory diagnostics. confirmatory tests are not always available in many parts of latam, especially in places where there is no veterinary diagnostic laboratory and practitioners may use human diagnostic laboratories. moreover, diagnostic tests, especially molecular analyses (i.e. reverse transcriptase polymerase chain reaction; rt-pcr), are sometimes too expensive, making the practitioner rely only on physical examination and sometimes also simple haematological examination. although diseases such as those caused by cdv and cpv2 infection are preventable by vaccination, in many latam countries they are still a problem because vaccination rates (i.e. "herd immunity") are too low and there is a high number of free-roaming dogs that have never been vaccinated (hartmann et al. 2007) [eb1] . another problem is that in some latam countries there is no requirement that vaccination be performed only by veterinarians. therefore, vaccination without clinical examination or without consideration of the quality and viability of the vaccine product is a common practice. it is also possible for a pet owner to purchase a vaccine from an agricultural merchant, without proper storage and handling, and administer it in their own home, without clinical examination by a veterinarian and without adequate transportation or maintenance of the product. regular clinical examination by a veterinarian including adequate vaccination of dogs with core vaccines is still an uncommon procedure among dog owners in many parts of latam. although there are no formal prevalence studies in most of the latam countries, there are theses and abstracts of studies in university library repositories, and some publications, showing that infectious diseases preventable by vaccination are still present in most of the countries. a meta-analysis of cross-sectional studies addressing the global prevalence of cdv showed that most of the articles from latam were from brazil, argentina and chile (costa et al. 2019) [eb1]. the prevalence of canine distemper in brazil was <10% to 41-50%, and in argentina from 31-40% to >70% when diagnosis was based on molecular studies. when studies were based on serology, seroprevalence ranged from 21-30% to 51-60% in chile and from 10-20% to >70% in brazil (costa et al. 2019) [eb1] . in the south of brazil, the seroprevalence of cdv was reported to be 27.3% (223/817) in non-vaccinated dogs (dezengrini et al. 2007) [eb1] . a study conducted between 2003 and 2004 in argentina found 73.8% of cases (73/99) were confirmed by rt-pcr in dogs with clinical signs of the disease. most of the dogs in that study were reportedly vaccinated against cdv, but had likely not received a full course of vaccination (calderon et al. 2007) [eb1] . other studies confirm that cdv is present in brazil (budaszewski et al. 2014 , monteiro et al. 2016 , alves et al. 2018 , chile (acosta-jamett et al. 2011 , colombia (espinal et al. 2014) , cuba (gonzález-chávez et al. 2017 ), ecuador (digangi et al. 2019 including the galápagos islands (levy et al. 2008 (calderón et al. 2011 (calderón et al. , 2015 , brazil (alves et al. 2018 , headley et al. 2018 , chile (acosta-jamett et al. 2015) , colombia (duque-garcía et al. 2017) , cuba (pino-rodríguez et al. 2018) , ecuador (levy et al. 2008 , aldaz et al. 2013 , de la torre et al. 2018 , digangi et al. 2019 , mexico (ortega et al. 2017) and uruguay (pérez et al. 2007 , puentes et al. 2012 , maya et al. 2013 [eb1]. although many veterinarians report that they see cases of canine infectious hepatitis (caused by canine adenovirus type 1; cav1) in latam countries, case reports with confirmation of the diagnosis are rare. one case report from argentina made a diagnosis based on history, macroscopic and microscopic evaluation and presence of hepatic inclusion bodies (lértora & burna 2003) (damián et al. 2005) [eb1]. in the galápagos islands, where canine and feline vaccines are prohibited, a seroprevalence for cav of 67.3% (64/95) and for cpiv of 100% (95/95) was reported in dogs (levy et al. 2008) there is little information regarding the prevalence of bordetella bronchiseptica infection in dogs in latam countries. b. bronchiseptica strains were isolated in 8.5% (11/130) of the nasal swabs obtained from 130 dogs in mexico (gonzález et al. 2006) [eb1]. although there are many studies showing a high seroprevalence of leptospirosis in dogs in latam countries, there are few publications where the agent was isolated in order to identify the serovar causing the disease. the microscopic agglutination test (mat) is the diagnostic test of choice for canine leptospirosis; however, it has poor ability to confirm the infecting serovar. studies involving isolation of leptospires from dogs are recommended for epidemiological purposes, as well as for selection of antigens for diagnostic assay development and vaccine design (sykes et al. 2010) [eb1] . during the vgg visits to latam countries, another commonly reported situation was the diagnosis of leptospirosis based on testing a single blood sample, sometimes considering the serovar with the highest titre as that causing the infection. although, in the presence of clinical signs, a single titre ≥800 can suggest infection, it cannot confirm a diagnosis. mat must be performed with paired serum samples collected 1 to 2 weeks apart. a fourfold change in titre supports a recent infection (sykes et al. 2010) [eb1] . the serogroup with the highest titre has been interpreted as the infecting serogroup; however, the highest mat titre can vary over time, indicating that the mat does not reliably predict the infecting serogroup in acutely infected animals (schuller et al. 2015) [eb1]. another problem in latam countries is the lack of standardisation and quality control in laboratories performing mat for diagnosis of leptospirosis, resulting in variation in results. leptospirosis in dogs is caused primarily by leptospira interrogans and leptospira kirschneri (sykes et al. 2010) [eb1]. however, leptospira noguchii (silva et al. 2009) [eb1] and leptospira santarosai (miotto et al. 2016) [eb1] were also isolated from dogs in brazil. leptospira interrogans serovars most frequently isolated from both sick and apparently healthy dogs in brazil were canicola and copenhageni (yasuda et al. 1980 , rodrigues et al. 2007 , miraglia et al. 2013 , hagiwara et al. 2015 [eb1]. l. interrogans serovar pomona was isolated from a number of dogs in one report (yasuda et al. 1980) [eb1] . l. interrogans serovar copenhageni was also the predominant serovar in isolates from suspected canine leptospirosis cases in trinidad and tobago (suepaul et al. 2010) . cases of human and canine rabies have been reduced by nearly 90% over the past 20 years in latam countries following active mass vaccination programmes (schneider et al. 2011) [eb1] . although costa rica, french guyana, guyana, panama, suriname and 7 uruguay are free of dog rabies, other countries still report cases (velasco-villa et al. 2017) [eb1] . according to the pan-american health organisation (paho) epidemiologic surveillance system for rabies, during 2010 to 2012, bolivia and haiti had the highest incidence of human rabies transmitted by dogs in the western hemisphere: 15% (6/40) and 40% (16/40) of all cases, respectively (vigilato et al. 2013) [eb1]. canine visceral leishmaniosis (cvl) is widespread from mexico to argentina, with autochthonous cases reported in many countries. the number of infected dogs in latam is estimated in millions, and there are high infection rates, especially in brazil (marcondes & day 2019) . most epidemiological studies are conducted using serology, but the application of pcr in endemic areas has confirmed that the prevalence of infection in dogs is much higher than the seroprevalence (baneth et al. 2008) . the seroprevalence of cvl in endemic areas of brazil ranges from 3.1 to 36.0% (rosypal et al. 2007 , belo et al. 2017 , marcondes & day 2019 the seroprevalence of cvl increased in paraguay between 2005 to 2016, with values ranging from 23% to 32% (miret et al. 2010 , portillo et al. 2011 . most cases were concentrated around the capital of the country, asunción, where the seroprevalence reached 69% in stray dogs in 2010 (miret et al. 2011) [eb1] . in 2006, when the first case of cvl was reported in argentina, the prevalence of cvl (based on serology and/or pcr) was 57.3% (cruz et al. 2010) [eb1] . in uruguay, a survey in salto, a city on the border with argentina, found 22% seroprevalence for leishmania spp. (satragno et al. 2017) [eb1]. studies of the seroprevalence of cvl in mexico, venezuela and colombia have reported levels between 1.7 and 15.7% (arjona-jiménez et al. 2012 , 5.6 and 40.0%, (zerpa et al. 2000 , 2001 , feliciangeli et al. 2005 and 1.6 and 36.0% (fernández et al. 2002 , cortés 2006 , rosypal et al. 2007 , paternina-gómez et al. 2013 , respectively [eb1]. few studies have been published in peer-reviewed journals with a confirmed diagnosis of this disease. in the south of brazil 69.1% (67/97) of cats tested were seropositive for fpv; 100% (11/11) of vaccinated cats, 66.6% (34/51) of unvaccinated cats and 62.8% (22/35) of cats with unknown vaccination history (johann et al. 2009) [eb1] . from 1996 to 2012, 1850 cats had necropsy examination at a university hospital in southern brazil. of these, 33 (1.78%) had a diagnosis of fpv infection confirmed by immunohistochemistry (castro et al. 2014) [eb1]. a study conducted in brazil (2004 brazil ( to 2005 of 51 faecal samples from 46 diarrhoeic and five asymptomatic unvaccinated domestic cats, confirmed fpv infection by pcr in six (11.76%) cats (garcia et al. 2011) [eb1] . few studies have been published in peer-reviewed journals with a confirmed diagnosis of fhv1, fcv or c. felis infection. a study of 302 cats from the south of brazil with and without clinical signs of respiratory disease, reported isolation of fhv1 and fcv with pcr confirmation in 11.2% (34/302) and 8.6% (26/302) of the cats, respectively (henzel et al. 2012) [eb1] . in another study of 108 unvaccinated kittens with and without conjunctivitis in brazil, 57.4% (62/108) had infection with fhv1, 37.0% (40/108) with fcv and 24.1% (26/108) with c. felis, confirmed by pcr (baumworcel et al. 2017) [eb1]. c. felis was also identified by pcr in 6.2% (9/145) (seki et al. 2010) [eb1] and in 58% (18/31) (gonsales et al. 2013) [eb1] of cats with clinical signs in two studies in brazil. most studies on the prevalence of felv and fiv infection come from brazil. although studies are available from university repositories in countries such as argentina, chile, guatemala and mexico describing high prevalence of felv infection, few of these have been published in peer-reviewed journals. in developed countries the prevalence of felv infection is usually low, but in some latam countries the prevalence appears to be high. the prevalence of felv infection reported in brazil varies according to the region studied, with values of 0.33% (1/302) by enzyme-linked immunosorbent assay (elisa) (sobrinho et al. 2011 ), 1.1% (1/90) by elisa (marcondes et al. 2018) , 2.6% (6/230) by immunochromatography (lacerda et al. 2017) , 11.52% (126/1094) by immunofluorescence antibody test (ifat) (almeida et al. 2012) , 22.26% (55/247) by elisa (biezus et al. 2019) , 32.5% (13/40) by elisa (teixeira et al. 2007) , 38.3% (46/120) by ifat (meinerz et al. 2010 ) and 47.5% (507/1072) by pcr (coelho et al. 2011) [eb1] . leukaemia was associated with felv infection in 78.4% (29/37) of the cases in a study conducted in brazil (cristo et al. 2019a,b) [eb1]. fiv prevalence in brazil appears to be lower than that of felv, with studies showing values of 3.33% (15/450) by pcr (caxito et al. 2006) , 4.14% (6/145) by pcr (teixeira et al. 2007) , 5.5% (5/90) by elisa (marcondes et al. 2018) , 5.63% (17/302) by elisa (sobrinho et al. 2011) , 5.84% (16/247) by elisa (biezus et al. 2019) , 6.1% (14/230) by immunochromatography (lacerda et al. 2017) , 6.1% (9/148) by elisa and pcr (teixeira et al. 2019 ) and 14.7% (67/454) by pcr (lara et al. 2008) in argentina, cats with clinical signs compatible with retrovirus infection were evaluated and fiv infection was confirmed by immunochromatography in 21.45% (55/255) and by pcr in 20.34% (52/255) of the cats, while felv prevalence was 7.64% (14/255) by immunochromatography and 11.82% (30/255) by pcr [eb1]. in the yucatan peninsula of mexico, the seroprevalence of retrovirus exposure in a population of cats was reported to be 2.5% (5/227) for fiv and 7.5% (17/227) for felv (ortega-pacheco et al. 2014) [eb1]. a study conducted on a chilean island found a prevalence of infection, by pcr, for felv of 33% (26/78) (mora et al. 2015) [eb1]. seroprevalence of retroviral exposure in a cross-sectional survey of a convenience sample of domestic cats from costa rica's greater metropolitan area was 16.7% (17/102) for felv and 8.8% (9/102) for fiv (blanco et al. 2009) [eb1] . seroprevalence of retrovirus exposure for cats living in a shelter in venezuela was 2.1% (2/95) for felv and 3.1% (3/95) for fiv (pino et al. 2015) [eb1]. a study conducted in colombia found a seroprevalence of 10.7% (184/1718) for fiv (molina et al. 2016 ) and a study in guatemala reported a seroprevalence of 16.7% (5/30) for felv (lickey et al. 2005) [eb1]. information on vaccines and vaccination practice was derived from our kol meetings, the questionnaire survey and practice visits. it is recognised that there is under-vaccination of the companion animal populations in the latam countries; e.g. our argentinian kols estimated that only 20 to 35% of owned pets were vaccinated and kols from brazil suggested that 17% of dogs and 6 to 9% of cats had an annual veterinary visit (and vaccination). small companion animal vaccines are available to practicing veterinarians throughout latam. there are two major sources for these products. the majority of vaccines are produced by the major global manufacturers and are either the same or related products to those marketed in other regions and countries by those manufacturers. such products are supported by north american and/or european licensing dossiers describing their quality, safety and efficacy, and often by independent peer-reviewed scientific literature. in this document, we will refer to such products as "international vaccines" or "quality assured vaccines." the second source of vaccines is, less commonly, national manufacturers of specific products. the vgg was unable to assess the quality, safety and efficacy of such products, which are generally unsupported by independent peer-reviewed scientific literature. for that reason, all of the recommendations made in this document (with the single exception of leishmania vaccines in brazil, which will be discussed specifically below) relate only to international quality assured vaccine products. however, although the majority of vaccine products are derived from the international manufacturers, there are different and much lesser product ranges available in the latam countries compared with markets in, for example, the united states or europe. there are: (1) fewer products from a manufacturer's range made available, (2) unique products from an international manufacturer that are unavailable in other regions (e.g. the giardia vaccine, which has been removed from most global markets with the exception of latam and will be discussed specifically below), (3) a trend to large multiantigen vaccines rather than the lesser antigen combinations that are now widely available elsewhere and (4) distinct differences with respect to licensed duration of immunity of the same vaccine product between markets elsewhere and markets in latam. all of these factors make it very difficult for veterinarians in latam to vaccinate in accordance with the current wsava global vaccination guidelines. in particular, the delivery of core vaccines to adult dogs and cats no more frequently than every 3 years is challenging when it is not possible to obtain three-component core vaccines (e.g. a combination of cdv, cav and cpv2 or a combination of fpv, fhv1 and fcv) and these are admixed with multiple non-core antigens in large multicomponent combinations. the challenge is compounded when the licensed duration of immunity (doi) for individual core antigens is 1-year, when the identical products in other markets carry a minimum doi claim of 3 years. as we have found elsewhere, there was a reluctance to accept that a 1-year licensed product might be used "off label" every 3 years (with informed client consent) even though the identical product is authorised in this way in other regions. this "transition stage" in the use of core vaccines was more readily embraced by veterinarians in north america and europe than it has been, or likely will be, in markets such as latam. as we found in asia, there are also challenges around rabies vaccination of individual pet animals in the practice setting (as opposed to government-run mass vaccination campaigns). rabies vaccination is mandated by law to occur on an annual basis and currently the international inactivated rabies vaccines carry a 1-year licensed doi in most latam countries. however, the identical products in other global markets now have a 3-year licensed doi. in order to progress in latam, manufacturers and regulators will need to work to extend the label claim for doi of these products, and at the same time, the veterinary professional associations will need to lobby for changes in the law (as has already happened in many other countries) so the law becomes consistent with the science. moreover, there remains a fundamental ethos in latam that a veterinary practice derives an important proportion of its income from the sale of vaccines to clients. repeatedly on our practice visits, we noted large sign boards above the reception desk in practices that listed individual dog and cat vaccines and their prices. it was clear that clients, with or without the advice of the veterinarian, would need to select the vaccines that their pet received on the basis of what they could afford to pay. the concepts of the "annual health check" and incorporating vaccination into a preventive health care programme for the individual pet (a practice "health care plan") were novel to many members of the veterinary community in latam. because of the perceived reliance on vaccine sales for underpinning practice income, there is also a current culture of "more is better." veterinarians almost exclusively deliver vaccination on an annual basis, using the vaccine product that contains the greatest antigen combination. clients have been accustomed to visiting their veterinarian annually for a "vaccine booster." annual administration of large multicomponent vaccines are deemed preferable because the client has been led to expect that this approach is superior. we were told repeatedly that veterinarians would "lose their clients" if they did not offer annual multicomponent vaccination with the highest number of antigens possible. there is something of a "vicious cycle" to this concept, because manufacturers continue to supply and promote multicomponent products that may include (for the dog) anything up to 10 different antigens. a further issue faced by veterinarians in latam is that companion animal vaccination is not restricted to the veterinary practice. pet stores are able to vaccinate puppies and kittens before sale and owners may obtain vaccines directly for administration to their pets using poorly-considered vaccination schedules. as the vgg had seen during our asian project, there are also common and simple issues related to "vaccine husbandry" in latam veterinary practices. these largely relate to the in-practice storage of vaccines which often takes place in multiuse domestic refrigerators with no temperature monitoring and storage of multiple medicines (and often food and drink for human consumption). during our asian project, the vgg produced some simple guidelines for effective vaccine husbandry and these are replicated and extended in the current document (table 3) for the benefit of latam practitioners. although the 2016 wsava global vaccination guidelines have been translated into spanish and portuguese, and are freely available from the wsava website, it was clear that most veterinarians (except for the kols) were not aware of these and had not read them. during our country visits there was often publicity in the veterinary press concerning the wsava project and the translations were promoted at our ce events. contemporaneous with the vgg latam project has been a project run by the federación iberoamericana de asociaciones de pequeños animales veterinarios (fiavac). the project is managed by the comité latinoamericano de vacunología en animales de compañía (colavac) and aims to produce vaccination guidelines that consider the epidemiological and cultural idiosyncrasies of veterinary practice in latam. the establishment of colavac is entirely within the spirit of wsava vaccination guidelines. the 2016 wsava guidelines clearly state that "these guidelines are not a mandatory edict, but rather should be used by national associations and individual veterinary practices to develop vaccination schedules relevant to the local situation." colavac is, therefore, an example of precisely that recommendation and we congratulate fiavac on this important initiative. colavac guidelines have now been released for brazil, argentina and mexico (http://www.fiavac.org/guias.php) and recently, in a scientific journal, for peru (rubio et al. 2018) ; however, readers will note that the guidelines differ in their recommendations for use of the same vaccines in the three countries, and sometimes differ from the recommendations made by the vgg in the present manuscript. there are some important reasons that might account for the latter observation and these relate to the ideal working practices for an expert group that produces practice guidelines. firstly, such expert groups must be completely independent of industry and should not include industry representatives on committees or have input or right of veto from industry sponsors. as readers may see from the conflict of table 3 . vaccine husbandry: key points for veterinary practitioners • vaccines should be kept in a designated refrigerator that is only used for storage of drugs and vaccines (not foodstuff or drinks) • the electricity supply to a vaccine refrigerator should be safeguarded against inadvertent breaks by use of a switchless electric socket or a plug clearly marked "do not switch off" • vaccines (and particularly adjuvanted vaccines) have an optimum storage temperature that is usually between 2 and 8°c (domestic refrigerators should be maintained at 4°c). these products should not be frozen or positioned adjacent to the freezer compartment of the refrigerator, and refrigerator temperature should be monitored regularly by use of a maximum-minimum thermometer located in the main body of the refrigerator. ideally, the temperature of the refrigerator should be charted in a log book on a daily basis • vaccines should be stored in the refrigerator with adequate room for air to circulate enabling a constant temperature to be maintained around the products • vaccines should be stored in the refrigerator within the manufacturer's packaging • certain shelves should be designated for specific vaccines and the location of vaccines listed outside the refrigerator. this will minimise the time the door is kept open while accessing vaccines • correct stocks of vaccines should be maintained, without overstocking • stock should be rotated so new stock is placed at the back • vaccines transported into the field should also be subject to continuation of the "cold chain." they should be transported in a cold box, but not put in direct contact with ice or ice packs • freeze-dried vaccines should be reconstituted immediately before use with appropriate diluent or liquid vaccine given concurrently (as per manufacturer's recommendations). it is bad practice and contraindicated to make up first thing in the morning the vaccines anticipated to be used during the day. some vaccine components (e.g. cdv, fhv-1) are particularly labile in this regard and so these vaccines may not induce adequate immunity if not reconstituted just before use • vaccines should only be mixed together in the same syringe if this is specified as acceptable in the manufacturer's data sheets • syringes and needles for vaccines should not be reutilized • vaccine injection sites should not be sterilised with alcohol or other disinfectant as this may inactivate infectious (mlv) vaccines • vaccines should be "in date" and precise details of batch numbers, components and site of injection should be noted in the animal's medical record interest statement that ends the present manuscript, the vgg is considered an entirely independent academic committee. secondly, guidelines should be evidence-based and supported wherever possible by peer-reviewed published scientific literature. the vgg developed an evidence-based hierarchy for the science of vaccinology (day et al. 2016) , which is applied to its global and now regional guidelines. finally, guidelines documents themselves should undergo scientific peer-review and be published in a creditable scientific journal rather than an industry magazine. vgg documents have always undergone such independent scrutiny and are published in the official scientific journal of the wsava, the journal of small animal practice. it is challenging to make recommendations regarding undergraduate education in an environment where there is such diversity in resources and standards between state-funded and private veterinary schools and a lack of any form of national curriculum. there is concern from the veterinary profession itself in the standards that might apply to the rapidly growing market in private veterinary education. the vgg can only emphasise the importance of solid grounding in the traditional teaching of veterinary immunology and microbiology as it pertains to small companion animal infectious disease and vaccinology, and to the development of tuition in client communication and delivery of vaccination in a clinical setting that must occur during the clinical years of a veterinary programme. those academics who teach such curricular elements should be encouraged to be well-versed in the wsava global vaccination guidelines. there is also clearly a huge need for postgraduate ce in small companion animal vaccinology. this is, to a large extent, the responsibility of the professional associations and veterinary industry and it is encouraging to see some of the initiatives for these subjects being incorporated into congress programmes and forming the content for postgraduate seminars in latam countries. the use of electronic delivery of tuition (i.e. via webinars) is also becoming more widespread in latam and vaccinology should comprise a valuable component of such programmes. the wsava itself hopes to further develop an on-line platform for delivery of ce in the near future and vaccination guidelines will form part of that content. it would be beneficial if discussions could be held in latam about moving towards compulsory continuing professional development for re-registration purposes for veterinary professionals. as can be seen from the summary of peer-reviewed scientific data related to small companion animal infectious diseases and vaccinology presented above, there is a marked lack of relevant information available to the veterinary profession in latam. given the very large numbers of academic institutions and academic staff devoted to tuition in microbiology and immunology, it is disappointing that there are few active research programmes in this important area of veterinary medicine. it is likely that this reflects a number of possible contributing factors: (1) that in private institutions there is a focus on teaching rather than research, (2) that it is challenging to obtain research funding for investigation of small companion animal infectious disease that does not have zoonotic potential (e.g. cvl, leptospirosis and canine rabies), (3) that greater academic kudos might be derived from investigating diseases of production animals and (4) that diagnostic laboratory infrastructure for undertaking infectious disease surveillance programmes is lacking. although much of the scientific literature reviewed by the vgg was generated in brazil, it is alarming to see, in that country, the current climate of governmental cuts in support for tertiary education and research, in particular for programmes that support the training of the next generation of veterinary research scientists via msc and phd studies. the vgg strongly supports the performance of clinically relevant research into small companion animal infectious diseases. in particular, developing a clear understanding of the regional prevalence of different infectious agents and the classification of infectious agents circulating in the field (e.g. specific serovars of pathogenic leptospires). there are clearly some distinctive aspects of infectious disease epidemiology in latam, in particular the observed higher prevalence of feline retroviral infections. only by generating current surveillance and molecular phylogeny data will there be advances in clinical diagnostics, vaccine availability and disease control. as we suggested in asia, there may be mutual benefit to academic researchers in veterinary schools working more closely with industry in order to generate clinically relevant data that might be used to introduce new vaccine products into latam for the benefit of the profession and the animals for which we care. as will become clear from the recommendations made below, there is a particular challenge facing the implementation of global vaccination guidelines in latam. this relates very simply to the lack of minimal-antigen product ranges that are widely available in north america, europe and other markets, and enable veterinarians in those countries to vaccinate in accordance with wsava guidelines. until there is a shift away from large multi-antigen vaccines (containing anything up to 10 different antigens) towards trivalent or bivalent core vaccines with monovalent or bivalent non-core vaccines, it will be challenging for latam practitioners to embrace the new standards in vaccinology that are now well-embedded in many other markets. once such product ranges are more widely available (currently only in argentina), it will then require significant education as to how they are best used in practice and a radical change in ethos to embrace the concept of preventive health care delivered through an annual health check or health care plan, as opposed to the deliberate marketing of vaccine products as commercial drivers of central importance in veterinary practice. an important challenge in making such changes lies in identifying who has responsibility for driving change. arguably, veterinary industry should lead in bringing revamped product ranges to latam, but this cannot happen without the support of the veterinary profession via the professional associations and without some flexibility in vaccine licensing requirements. with respect to the latter, the vgg supports the acceptance of licensure studies performed for other markets in obtaining new licences in new markets. at very least, not having to perform additional studies for products that are already licensed in north american or european markets would provide significant animal welfare benefits. there remains the significant challenge of veterinary vaccines being available directly to owners and breeders out with the veterinary practice. a change in emphasis from the veterinary practice simply selling vaccines to selling a holistic preventive health care package based in professional advice will be required in order to re-educate the pet-owning public and attract them back to the veterinary practice. the vgg recommends that veterinarians in latam implement the basic principles of evidence-based companion animal vaccinology presented in the 2016 wsava global vaccination guidelines (table 4 ; day et al. 2016) [eb1] . understanding the concept of core versus non-core vaccines is fundamental to application of the vaccination guidelines in practice. core vaccines are those that every dog, regardless of location or lifestyle, must receive for protection against infections that cause significant morbidity or severe or fatal disease. core vaccines contain cdv, cav2 and cpv2, preferably as modified live viruses (modified live vaccine; mlv). in countries where canine rabies remains an endemic disease, inactivated rabies vaccine is also regarded as a core vaccine for every dog. non-core vaccines are those considered for individual animals whose geographical location or lifestyle puts them at risk for specific infections. non-core vaccines are not required for every animal and should not be used where there is no evidence for existence of a related disease or when the risk for exposure is minimal. non-core vaccines include leptospira vaccines and vaccines designed to protect against elements of cirdc, which usually contain b. bronchiseptica with or without cpiv. the wsava global guidelines classify some vaccines as not recommended for any dog because there is insufficient scientific evidence to justify their use. these include the inactivated canine enteric (non-pantropic) coronavirus (enteric ccov) vaccine and the giardia vaccine when used to either prevent or treat infection. non-core vaccines are generally given annually unless the datasheet specifically recommends otherwise. felv vaccines may be given every 2 or years to adult cats (and some qualityassured felv vaccines carry a licensed 2-or 3-year doi in markets outside of latam) [eb1] not recommended vaccines these include vaccines against coronavirus (canine or feline), giardia and microsporum canis the generic information in this table should be read in conjunction with the more detailed recommendations provided in the current wsava vaccination guidelines (day et al. 2016) . vaccination according to wsava guidelines is possible only where available product ranges separate core from non-core vaccine components. note that these recommendations apply only to quality-assured vaccines, most of which are produced by large, international companies. ccov is considered of minor clinical importance as a primary enteric pathogen, causing only mild diarrhoea in puppies. more severe enteric disease occurs with ccov and cpv2 coinfection (decaro et al. 2004) [eb1] . published studies have demonstrated that commercial inactivated enteric ccov vaccines induce only transient serum antibody responses and do not reduce viral infection or faecal shedding of virus compared with non-vaccinated dogs (pratelli et al. 2003 , de castro et al. 2010 [eb1]. moreover, injectable ccov vaccine does not lead to elevation of faecal ccov-specific iga antibody concentration, which is believed to underlie immune protection (decaro et al. 2004) similarly, dogs vaccinated with a commercial inactivated giardia vaccine were not protected from giardia infection in that there were no differences in parasite cyst or antigen detection rates or the occurrence of diarrhoea between vaccinated and unvaccinated dogs (anderson et al. 2004 , lund et al. 2010 [eb1]. in addition, treatment of giardia-infected animals with a commercial inactivated giardia vaccine was not effective in eliminating cyst production (anderson et al. 2004) the wsava guidelines recommend revaccination of puppies with international mlv core vaccines at timed intervals over the first 4 months of age to overcome interference by maternally-derived antibody (mda) [eb1] . the guidelines also recommend that a final mlv core vaccine is given between 6 months to 1 year of age in order to ensure that all puppies receive at least one dose of vaccine that is able to confer immunity in the absence of mda [eb4]. development of protective immunity is not dependent on the number of mlv core vaccines given during the puppy vaccination series, but rather when they are given. for adult animals, there is ample evidence supporting revaccination with quality-assured international mlv core vaccines no more frequently than every 3 years (abdelmagid et al. 2004 , bohm et al. 2004 , mouzin et al. 2004 , gore et al. 2005 , schultz 2006 , larson & schultz 2007 , mitchell et al. 2012 , killey et al. 2018 [eb1]. while regulatory authorities in latam countries require annual revaccination with international mlv core vaccines licensed elsewhere for use at 3-year intervals, this practice is regarded as inappropriate use of client financial resources that are better applied to annual wellness examinations, routine parasite prophylaxis, and treatment of medical issues. increasing the frequency of vaccination with mlv core vaccines does not confer greater protection to an individual animal. increasing the number of animals that are properly vaccinated is much more important to ensure protection through population or "herd" immunity than vaccinating each animal more often. even though the 3-year doi datasheets for quality-assured international mlv core vaccines are not currently accepted by latam countries, the vgg encourages the national and local regulatory authorities to permit practitioners to use these vaccines according to the wsava guidelines as "off-label use" products with informed client consent. this approach has been used successfully in other countries pending acceptance of the quality-assured international vaccine datasheets by the national and local authorities. issues with vaccine product availability, product licensed doi, and knowledge of disease prevalence and exposure risks hampers adoption of the wsava global vaccine guidelines by practitioners in latam countries. in many of these countries, there is limited availability of quality-assured multicomponent and single-component international vaccines allowing separate use of mlv core antigens versus non-core antigens. the paucity of peer-reviewed studies on specific disease prevalence in latam countries presents challenges for practitioners in making evidence-based decisions on what non-core vaccines are appropriate for individual animals in different regions. latam practitioners and their national associations should lobby industry and government regulators for access to quality-assured international canine vaccines that contain just the mlv core components (cdv, cpv2, cav2) or the non-core components (leptospira, cpiv, bordetella). this will allow for administration of the mlv core vaccine every 3 years and for separate annual vaccination with non-core vaccines for individual dogs at risk. currently, most quality-assured international vaccines available in latam countries contain mlv core antigens (cdv, cav2, cpv2) combined with non-core antigens (leptospira) and non-recommended antigens (i.e. enteric ccov). practitioners can follow some pragmatic recommendations presented in table 5 to transition from giving these multicomponent vaccines every year to every dog to using the core and non-core vaccines separately according to the wsava guidelines. included in this transitional pragmatic protocol is the "off-label" administration with client consent of mlv core vaccine components every 3 years to adult dogs instead of annually. the vgg recognises that practitioner use of this pragmatic protocol is limited by local product availability. for clients that can only afford one vaccine for their dog, the recommended approach is to choose a quality-assured international vaccine containing the mlv core components and give that vaccine at a time when the single dose can induce long-lasting protective immunity in the absence of maternal antibody interference (i.e. at 4 months of age or older). canine visceral leishmaniosis (cvl) caused by leishmania infantum is one of the most significant zoonotic diseases in latam and the geographical distribution of cvl is expanding in the region. cvl is widespread from mexico to argentina, with autochthonous cases reported in many countries (marcondes & day 2019) [eb1]. although vaccines can prevent active infection and the risk of development of clinical disease in some dogs, some vaccinated dogs can become progressively infected and transmit the parasite to the sand fly vectors even in the absence of clinical signs (bongiorno et al. 2013 , fernandes et al. 2014 , oliva et al. 2014 , regina-silva et al. 2016 [eb1]. therefore, for animals living in endemic areas, from an epidemiological viewpoint, it is more important to use insecticides, especially collars, to prevent sand fly bites, than it is to vaccinate (sevá et al. 2016 , lopes et al. 2018 . whenever possible, the two measures should be combined, in order to provide a high level of protection not only for dogs, but for other animals and people that share the same environment. it is important to highlight that a previous history of vaccination does not exclude a diagnosis of cvl in dogs with clinical signs or clinicopathological abnormalities suggestive of the disease. currently in latam there are only two licensed vaccines against cvl. one contains the recombinant a2 protein of l. donovani in an adjuvant, licensed in brazil and paraguay, and the other consists of purified excreted-secreted proteins of l. infantum (liesp) in an adjuvant, and is licensed in paraguay and argentina. the vaccination protocol for puppies includes three doses given 3 weeks apart and an annual booster. the a2 vaccine can be used in dogs from 4 months of age and the liesp vaccine from 6 months of age. adult dogs that have never been vaccinated receive the same protocol. vaccines against cvl should only be considered for dogs living in endemic areas, where they are at risk of being infected. according to the manufacturer's recommendations, only seronegative dogs should be vaccinated; however, many dogs can be infected without seroconversion, and therefore, be improperly vaccinated. it is clear that large-scale mass vaccination programmes conducted over recent decades have succeeded in controlling canine rabies virus infection in dogs and cats (and therefore the human population) in many latam countries. there are, however, remaining "hot spots" for disease and low numbers of individual cases are recorded in countries with good overall control. in most latam countries there is ongoing surveillance and legally-mandated annual canine rabies vaccination. this may be delivered by mass vaccination field campaigns run by government or non-governmental organisations or through the veterinary practice for individual client-owned pet animals. vigilance and continued vaccination to maintain herd immunity are essential at this time for maintaining control of canine rabies. as discussed above, there is a disconnect between the law and the science pertaining to rabies vaccines. there is no doubt that non-core vaccines are generally given annually unless the datasheet specifically recommends otherwise; felv vaccines need not be administered to adult cats on an annual basis (see table 4 ) not recommended vaccines these include vaccines against coronavirus (canine or feline), consider whether there is sufficient scientific evidence to support their use the generic information in this table should be read in conjunction with the more detailed recommendations provided in the current wsava vaccination guidelines (day et al. 2016) . note that these recommendations apply only to quality-assured vaccines, most of which are produced by large, international companies. in mass vaccination field campaigns (particularly where these aim to vaccinate free roaming stray or community owned dogs) annual revaccination is essential to account for population turnover. however, for a client owned, veterinarian-visiting individual pet animal, vaccination with an international quality-assured canine rabies vaccine should confer a minimum 3 year duration of immunity (day et al. 2016) [eb1] . a move to licensing those vaccines with a 3-year doi as the same products have in the usa, canada and europe would help address this anomaly. feline vaccination: aspirational protocols when aspiring to produce an optimised vaccination protocol for cats in a particular locale, the immensity and diversity of latin america must be borne in mind. nevertheless, it is possible to provide broad advice to latam veterinarians based on what has been learned about feline infectious diseases in the region and beyond, and by considering what vaccines are commercially available in latam. veterinarians in all latam countries are encouraged to follow the fundamental advice provided in the latest wsava vaccination guidelines (day et al. 2016) (table 4 ). as these guidelines make clear, there are core vaccines that, in an ideal world, all pet kittens should receive and all adult cats should receive sufficiently frequently to ensure protection throughout life. these vaccines protect against infectious agents that can cause severe illness or death, especially in kittens. in all countries, vaccines against fpv, fhv1 and fcv are considered core (scherk et al. 2013 , day et al. 2016 . in countries where rabies is endemic, rabies vaccines are also regarded as core (scherk et al. 2013 , day et al. 2016 [eb1]. in addition, there are non-core vaccines. not every kitten or cat need necessarily receive every one of the non-core vaccines. use of these vaccines should be based on an informed risk-benefit analysis, based on knowledge of local disease frequencies and the lifestyle of the individual cat (day et al. 2016) [eb1]. non-core vaccines protect against infectious agents that may be encountered frequently in some areas, but are known to be rare or absent in other places (e.g. felv). some non-core vaccines (e.g. those against c. felis infection) protect against disease agents that are generally less pathogenic than those covered by the core vaccines or are treatable using antibiotics. the vgg categorises one feline vaccine (against fip) as "not recommended." although this is a commercially-available vaccine in some countries (not in latam), the vgg has judged that there is insufficient evidence of benefit to recommend its routine use. in some latam countries (e.g. brazil) felv has been reported to be highly prevalent in some regions (i.e. the southeast and deep south of the country) and much less prevalent in others, such as the north (almeida et al. 2012 , lacerda et al. 2017 , biezus et al. 2019 , cristo et al. 2019a [eb1]. overall, felv prevalence in brazil seems to be considerably higher than in many other countries where its prevalence has been studied (galdo novo et al. 2016) [eb1]. in mexico, felv prevalence has been shown to exceed that of fiv in merida, tropical mexico, but does not match the very high prevalence values reported from various parts of brazil (ortega-pacheco et al. 2014) [eb1]. therefore, it is recommended that latam veterinarians seek to establish felv prevalence in their local area, to allow evidence-based decisions to be made about the recommended use (or otherwise) of felv vaccines. this is the essence of how non-core vaccines should be used. high-quality, mlv fpv vaccines have been shown to provide long-lasting, robust immunity to a large majority of vaccinated cats when used in accordance with wsava vgg guidelines , barrs 2019 [eb1]. as a precaution, revaccination every 3 years is generally recommended. vaccinating more frequently than every 3 years with high-quality mlv fpv vaccines is unlikely to provide any improvement in the degree of protection provided by these vaccines and may increase the risk of adverse reactions. it is far more important to ensure that a large proportion of the target population is vaccinated (i.e. to increase the overall herd immunity) than it is to increase the frequency of revaccination of individual animals in the population at risk. indeed, the unhelpful annual revaccination of cats against fpv with products, known to provide many years of protection, should be viewed as poor use of potentially limited client financial resources. these could be better applied to address other health issues in the pet and perhaps could be used to purchase non-core vaccines, if use of one or more of those is supported by evidence and hence justifiable in that locale. high-quality mlv vaccines against fcv and fhv1 do not provide such robust or long-lasting protection as do the fpv vaccines just mentioned (jas et al. 2015) [eb1]. the immunity conferred by these vaccines cannot prevent infection or development of the carrier state. nevertheless, for cats living "low risk" lifestyles (i.e. indoor only cats that do not visit boarding catteries) vaccination every 3 years is considered to provide sufficient protection (scherk et al. 2013 , day et al. 2016 . for cats at higher risk of fcv or fhv infection (i.e. cats with outdoor access or cats regularly visiting a boarding cattery), annual revaccination is recommended [eb4] . in some countries, it is possible to purchase vaccines that contain only fcv and fhv1, so that trivalent vaccines can be used every 3 years (fcv, fhv1, fpv) and a bivalent vaccine (fhv1, fcv), if needed, in each of the intervening years. unfortunately, such products are not, as yet, consistently available throughout the world. rabies vaccines must be used in accordance with local regulations. notably, some international quality assured rabies vaccines for use in cats provide protection for at least 3 years (jas et al. 2012) [eb1]. in the usa, regulations requiring annual revaccination of cats, despite evidence of much longer-lasting protection by some vaccines, were challenged and changed as a consequence of effective political lobbying by the veterinary profession and pet owners. a crucial feature of an idealised vaccination protocol for cats in any country would include a finish to the kitten series no earlier than 16 weeks of age. this is because evidence has accumulated in recent years indicating that a sizeable minority of kittens have significant amounts of interfering maternal antibodies against some of the vaccine components, even at up to 20 weeks of age (digangi et al. 2012 , jakel et al. 2012a [eb1]. a 16 weeks or later finish is consistent with this scientific evidence and with the current wsava vaccination guidelines, as well as with guidelines from other organisations. vaccine products available in latam countries may not carry datasheet recommendations for use as described in this section. it would be helpful if local regulations and guidance from veterinary professional organisations enabled practitioners to use vaccines "off label" with informed client consent. this approach was used for years by veterinarians in other countries, before datasheet recommendations were eventually updated. the vgg hopes that, in due course, quality assured core mlv vaccines produced by large, international pharmaceutical companies will have datasheet changes made in the latam countries. feline vaccination: pragmatic protocols small animal practitioners in latam countries are currently unable to adopt the wsava vaccination guidelines in full. this is for a number of reasons. firstly, rational use of non-core vaccines is hampered in many parts of latam by a lack of information about disease frequencies. conversely, for some regions, excellent, detailed information is available. where evidence is lacking, veterinarians often decide to take a precautionary approach. this can lead to unnecessary overuse of non-core vaccines. more research and surveillance would enable more informed, selective use of non-core vaccines. secondly, in many latam countries there is limited product availability. in particular, core vaccines licensed and approved for biennial, triennial or less frequent use are unavailable in many latam countries. in part, this may be because of a lack of locallygenerated evidence for extended doi and a requirement for such evidence from local regulatory authorities. yet multiple strands of evidence, generated in numerous countries, support a view that feline core vaccines can be used in latam countries similarly, and with as much confidence, as in other parts of the world. although current datasheets for many quality assured mlv core vaccines recommend annual revaccination of adult animals, the very same vaccines are given triennially in many other countries, including some with high infectious disease pressure. another challenge concerning product availability in latam is a paucity or lack of monovalent non-core vaccines. for example, in some countries, c. felis vaccines are only available in combination with the core fpv, fhv1 and fcv components and felv is only available in combination with the preceding four. therefore, there exist 3-component, 4-component and 5-component feline vaccines, but few or no monovalent, non-core products. a veterinarian who wished to protect against felv as well as the core agents, but perceived no need to protect against c. felis, might thus be forced to administer the c. felis component, even if it was judged superfluous. veterinary practitioners and regional associations should therefore continue to lobby industry and government regulators for changes that would bring recommendations concerning use of quality assured vaccine products into line with those that apply and are used in many other parts of the world. table 5 presents some pragmatic recommendations concerning use of feline vaccines that are intended to assist latam practitioners to head in the recommended direction. application of preventive health care plans with an annual health check to latin america as discussed earlier in this document it was clear from our discussions and practice visits in latam that the dominant culture in veterinary practice is that veterinarians sell vaccines to clients, that the sale of vaccines is the main driver for client attendance at the veterinary practice, and that vaccine sales underpin a large component of veterinary practice income. indeed, some 25 years ago, these were global principles that also applied to veterinary practice in north america, western europe, australia, new zealand, south africa and other developed markets. in the latter markets, in 2019, this culture has now been substantially replaced by a new way of promoting veterinary services (including vaccines) to clients. there has been a progressive move away from the concept of the "annual vaccination booster" or the "vaccine booster consultation" towards the implementation of holistic preventive health care packages delivered in part by an "annual health check" consultation. in more developed markets, this has now been extended to delivery of a practice "health care plan" for which a client might pay a regular monthly fee to cover numerous elements of preventive health care for their pets. the annual health check consultation is considered to require a longer period of time than a general consultation and provides the opportunity for the veterinarian to engage with the client to discuss in detail the overall health and wellbeing of the companion animal family member. elements of the health check consultation (or of an annual health care plan) might include consideration of nutrition, dental health, behavioural issues, endo-and ectoparasite control, vector-borne diseases testing and which vaccines (core or non-core) might be delivered during this annual visit. indeed, in many mature markets, annual assessment of the need for core revaccination (cdv, cav and cpv2 for dogs and fpv for cats) is now determined by in-practice serological testing ("titre testing") to determine whether an animal is already protected and therefore need not be revaccinated. the wsava global vaccination guidelines mention the value of serological testing and provide strong support for this approach. there is increasing literature to support the use of such serological tests in veterinary practice (e.g. killey et al. 2018) [eb1]. moreover, there is a substantial literature that evaluates the annual health check consultation and advises on the content, timing and approach to such a consultation (e.g. belshaw et al. 2019) [eb1] . implementing this new approach to delivery of companion animal preventive health care may be daunting for many latam practitioners. however, these changes need to be embraced in order for the profession in latam countries to keep pace with colleagues in more developed markets. whilst there may be a longer transition period for veterinarians working with economically constrained clients, these new concepts should be more readily embraced by those working in areas of relative prosperity. the vgg gratefully acknowledges the numerous kols in argentina, brazil and mexico who travelled to meet with us, often over long distances, to share their knowledge and expertise. we also thank the veterinarians in those countries who allowed us to visit their practices and the many veterinarians who completed our questionnaire survey. we are grateful to our colleagues from msd animal health, at the global, regional and national levels, who undertook all of the logistics for our country visits and we particularly thank them for the work involved in organising the ce events in each country. the work of the vgg has been supported financially by msd animal health who are global partners with the wsava. the vgg is an entirely independent group of academic experts who have authored this manuscript without consultation with industry. representatives of the sponsoring company do not attend vgg meetings. the company does not have the right of veto over vgg recommendations. questions about vaccine products the vgg does not recommend this vaccine because there is insufficient scientific evidence to justify its use. the evidence that canine enteric coronavirus is a primary pathogen leading to intestinal disease in adult dogs is weak; the diarrhoea associated with infection is mild unless there is concurrent infection with cpv2. experimentally, the virus causes only mild diarrhoea, if any, in dogs over 6 weeks of age and vaccination against cpv2 alone appeared to protect against challenge by both viruses. there is no evidence that available vaccines would protect against pathogenic, mutant forms of the virus that occasionally arise and have been described. there is even less evidence that the vaccine can protect against infection in the field and injectable vaccine does not appear to induce protective faecal iga antibodies (decaro et al. 2004) . brazilian data shows no difference in the identification of canine enteric coronavirus by pcr from the faeces of normal dogs and dogs with diarrhoea (gizzi et al. 2014) [eb1]. the vgg does not recommend this vaccine because there is insufficient scientific evidence to justify its use. the evidence that the vaccine can prevent either shedding or infection is weak. one large field study of 6000 dogs showed that vaccinated puppies were actually more likely to have diarrhoea than unvaccinated puppies, and there was no difference between these groups with respect to cyst or antigen detection (lund et al. 2010) [eb1]. the disease in dogs is not life-threatening, is rarely zoonotic, is of low prevalence and responds to therapy; for these reasons the vaccine is not recommended for client-owned dogs. it is not known whether the vaccine can cross-protect against strains of giardia other than those used in challenge studies. brazilian data shows no difference in the identification of giardia by pcr from the faeces of normal dogs and dogs with diarrhoea (gizzi et al. 2014) [eb1] . it is notable that the vaccine has been withdrawn from all markets globally with the exception of those in latam. although published studies addressing this question do not always agree, the vgg is of the belief that, immunologically, vaccination via a mucosal route is more likely to generate relevant protective immunity (specifically the production of mucosal iga and igg antibodies as opposed to systemic igg antibodies) for pathogens that infect via the same mucosae (larson et al. 2013) [eb1]. intranasal vaccination may have the added benefit of a rapid onset of immunity that may relate to a non-specific stimulation of innate immunity (via toll-like receptor engagement and local cytokine/chemokine production) [eb4]. this may be beneficial when a dog is to be exposed in the short term to an environment where there is a risk of exposure to elements of the canine infectious respiratory disease complex (cirdc). intranasal vaccines may be used in puppies as early as 3 weeks of age as a single dose, with annual revaccination required. intranasal vaccines are available (depending on the market and not all in latam) that are specific for b. bronchiseptica (bb) alone or bb in combination with cpiv, or bb in combination with cpiv and cav2. oral vaccines against bb are available in australia, north america and europe. these products have the advantage of ease of application, but contain only a single antigen (bb) and may not share the same rapid onset of immunity as intranasal products. they may be given to puppies from 8 weeks of age and require annual revaccination. there is variation in the scientific literature as to whether the oral and intranasal bb vaccines confer equivalent protection, or whether protection is better with intranasal products (larson et al. 2013 , ellis et al. 2016a , scott-garrard et al. 2018 [eb1]. as to why these products are not available in latam, you would need to ask the manufacturers and regulatory authorities responsible for vaccine licensure. the vgg classifies leishmania infantum vaccines as non-core, meaning that their use should be restricted to dogs at risk in areas endemic for the infection. leishmania vaccines are only available in brazil, argentina and paraguay. these vaccines should be regarded as one tool in the prevention of canine visceral leishmaniosis. control of the access of susceptible dogs to sand flies (e.g. by housing indoors during the times of greatest sand fly activity) and the use of sand fly preventives (e.g. collars) is far more important than vaccination (sevá et al. 2016 , lopes et al. 2018 [eb1]. vaccines do not produce sterilising immunity; they may prevent or lessen the severity of clinical signs in infected animals, but do not always prevent infection and so even vaccinated dogs may act as a reservoir for leishmania (regina-silva et al. 2016) [eb1]. dogs should be tested before vaccination as vaccination of a dog that is already infected is of no benefit in the prevention of infection and a waste of vaccine. borrelia of different species are associated with infection and disease of dogs and cats in north america and europe through to asia. borrelia are transmitted by ixodes spp. ticks and have wild mammal and avian reservoirs. in order to introduce a borrelia vaccine to latam, there would need to be robust research studies into whether the pathogen exists in this region, whether there are competent tick vectors and wildlife reservoirs, and whether dogs and cats could become infected and go on to develop clinical signs of disease. in brazil, studies have identified borreliosis in human patients with brazilian lyme-like disease or baggio-yoshinari syndrome (yoshinari et al. 2003 , mantovani et al. 2012 , and borrelia burgdorferi sensu lato in asymptomatic humans (gonçalves et al. 2015) and ticks from the genus dermacentor (gonçalves et al. 2013) [eb1]. few reports relate to companion animals, and although anti-borrelia antibodies have been found in dogs, to our knowledge the pathogen has not been isolated from sick dogs (spolidorio et al. 2010 , nascimento et al. 2016 [eb1]. on that basis, there is currently no basis on which to justify introduction of a companion animal borrelia vaccine to the region. modern high-titre international quality-assured vaccines are more likely to be able to do this, which is why the vgg recommends use of such products. where available, the use of high-titre combination cdv and cpv2 vaccines designed for use in young puppies is also recommended where core vaccination is started earlier than 8 weeks of age (see tables 4 and 5 ). however, there is no guarantee that every puppy will make an early, active immune response to each vaccine antigen and so the global wsava guidelines should be followed: by giving the final early-life dose of core vaccine at 16 weeks of age or older with a follow-up vaccine between 6 and 12 months of age. this situation was faced by veterinarians globally in the last two decades when guidelines recommendations were for adult core revaccination no more frequently than every 3 years, but products all had a licensed duration of immunity of 1 year. at that time, veterinarians were able to use the available products in accordance with guidelines simply by obtaining informed client consent (and documenting this in the medical record) for "off label" use of the product. there was never any legal claim brought successfully against a veterinarian for doing this, nor examples of dogs contracting infection because of extending vaccination intervals. subsequently, in many markets globally, the identical core vaccines were relicensed with a 3-year doi. until this relicensing occurs in latam, veterinarians can adopt the same strategy that was used very successfully over the last 20 to 25 years in north america, europe and other regions. over the decades since the first identification of cpv2 in 1978, new biotypes of the virus (cpv2a, cpv2b and cpv2c) have emerged in many parts of the world, including latam. these virus variants are characterised by subtle changes in amino acid sequence in the vp2 protein. most vaccines contain either cpv2 or cpv2b and questions have been raised as to whether these provide adequate cross-protection against new virus variants (specifically cpv2c). there are numerous studies that show such crossprotection occurs and that all current cpv vaccines remain efficacious in the field (e.g. spibey et al. 2008 , wilson et al. 2014 [eb1]. occasional reports occur of clinical parvovirosis in vaccinated dogs, but this scenario generally relates to failure to vaccinate according to guidelines recommendations or vaccination of puppies that are already incubating the virulent virus. while there is no doubt that leptospirosis occurs in dogs in latam, there is minimal high-quality scientific evidence about the geographical distribution, causative serovars and clinical manifestations of the disease. the major weakness in many published studies is that the gold-standard for confirming clinical diagnosis (i.e. paired serology 2 weeks apart by the microscopic agglutination test [mat] ) and identifying the infecting serovar (isolation of the organism) has not been used. available studies do suggest that the dominant serovars circulating in the field in latam may still be l. interrogans serovars canicola and copenhageni [eb1] , and that consequently, the traditional canine "l2" vaccines containing these organisms might confer adequate protection. in north america and europe, "l3" and "l4" vaccines have been marketed to help address a greater diversity of causative serovars in those regions. at present, there is insufficient evidence on which to formulate a specific latam vaccine or to recommend adoption of the north american l4 products in an evidence-based fashion. where there is solid scientific evidence (see question 10) that leptospirosis is a significant clinical problem then it makes perfect sense to routinely vaccinate at-risk dogs to prevent a serious and potentially zoonotic infectious disease. however, it is simply not possible for the vgg to classify leptospira vaccines as core in our global guidelines, because there are parts of the world in which the infection does not exist or is of very low prevalence. moreover, the lifestyle of some individual dogs does places them at lower risk of encountering this infection. this is why the vgg promotes the use of non-core vaccines based on regional disease surveillance data coupled with a lifestyle history of the individual pet. latam practitioners must do their best to obtain reliable local data on leptospira infection to help inform decision making about use of this vaccine. decision making about whether or not to use non-core leptospira vaccines would be facilitated by robust surveillance data indicating whether leptospira was prevalent in your geographical area and which serovars were circulating in the field. unfortunately, such data are not available in most parts of the world. consequently, the decision to vaccinate needs to be taken based on the lifestyle of the individual dog. apartment dwelling dogs with limited and controlled access to outdoors are unlikely to require leptospira vaccination. however, dogs with outdoor access and particularly those with access to water that might be contaminated via exposure to rodents or domestic livestock should be vaccinated. even dogs kept in a yard may be at risk if small wildlife (e.g. rodents) can also access the yard. the prevalence of felv was much higher in europe 30 to 40 years ago than it is today. it is thought that the combination of (1) diagnostic testing for felv (which has become considerably more convenient and accurate over those decades), (2) suitable management of cats found to be infected and (3) widespread vaccination against felv, have together led to the substantial decrease in felv prevalence in some countries (studer et al. 2019) [eb1]. the first step in regions of latam where felv has not been well studied would be to determine local felv prevalence. if testing is considered impractical or too expensive, then it may help to recall that high prevalence of feline multicentric lymphoma, cranial mediastinal lymphoma and very severe non-regenerative anaemia are strong clues that felv may be prevalent in the area. in regions where many cats are known to become infected each year, client education and widespread vaccination should be practiced. ideally, cats should be tested prior to first vaccination because there is no benefit to vaccinating a cat that is already infected when that dose of vaccine may benefit another animal. this decision should be based on a risk-benefit analysis. if felv is known or highly suspected on the basis of good information to be prevalent in the town or region where you work, use of the non-core felv vaccine can be justified. for example, if there is a high prevalence of strongly felv-associated diseases, such as multicentric or cranial mediastinal lymphoma, increased pressure on owners to permit testing and vaccination against felv (in addition to use of core vaccine) is justified. each has its own advantages and disadvantages. if it is judged necessary to vaccinate a pregnant or immunosuppressed cat (e.g. a retrovirally-infected cat), an inactivated vaccine is considered safer from first principles (although the evidence for this is limited and recent studies suggest this may not be the case; bergmann et al. 2018) [eb1] . similarly, where there may be a multi-cat establishment without a history of upper respiratory tract infection, use of a killed product (from first principles) would reduce the risk of transfer of live vaccine virus. in some countries, inactivated vaccines are used in more cats than are mlv vaccines. in many other countries, mlv feline vaccines are used in far more cats than are inactivated vaccines. although it is considered uncertain and controversial by some experts, there is evidence that adjuvant (present in inactivated and subunit vaccines but generally not in mlv vaccines) is implicated as being associated with development of the feline injection site sarcoma (fiss) (abdelmageed et al. 2018 , kass 2018 [eb1]. this would be an important disadvantage of adjuvanted vaccines. there is some limited evidence that inactivated fhv1 vaccines provide more rapid onset of protection than do mlv fhv1 vaccines (lappin 2012) [eb1]. finally, where canine rabies is an endemic disease and cats should receive rabies vaccination as core, use of inactivated adjuvanted vaccine is the only option, unless there is access to a recombinant product. the vgg does not make recommendations about specific commercial brands of vaccine or generally about classes of vaccine. in some parts of the world there are recombinant virus-vectored vaccines available to protect against cdv, felv and rabies. in some circumstances these do have advantages: for example for use in wildlife species and as a means of avoiding use of adjuvanted rabies vaccine in cats, as these are one possible injectable product (of many vaccines and non-vaccine injectables) that have been associated with fiss (see questions 15, 67 and 68). to our knowledge, such monovalent products are not available in latam. rabies vaccines are routinely administered to individual pet animals visiting the veterinarian only every 3 years in north america and europe. in those regions the legal requirement is for triennial revaccination of adult dogs and cats. the international qualityassured rabies vaccines used in those regions all carry a licensed doi of 3 years. the licence is based on firm scientific evidence and licensing studies (e.g. lakshmanan et al. 2006) [eb1]; without such evidence the laws would not have been changed to allow 3-yearly revaccination. unfortunately, the identical rabies vaccine products, used in asia, africa and latam are administered annually. this is because the regional or national laws have not changed and industry has not relicensed the products with a 3-year doi as has occurred in north america and europe. in latam, you are still legally obliged to give rabies vaccines on an annual basis; however, the veterinary profession should be lobbying for change in the laws and relicensing of the vaccine products. you should also note that this only applies to individual pet animals visiting the veterinarian for vaccination. in the context of mass vaccination campaigns in the field (as might be conducted by government authorities or non-governmental organisations), rabies vaccines are still administered annually to as many dogs as possible (including to free-roaming dogs). this is because there is generally high population turnover in free-roaming dog populations and annual revaccination is required to maintain herd immunity levels of 70% [eb1]. this is a frequently asked question throughout the world. vaccines are unlike pharmacological drugs and are not administered on a mg/kg basis. vaccines contain a defined amount of antigen, which is the amount required to stimulate a primary or secondary immune response in an animal. each individual person and animal has an "immunological repertoire" of antigen-specific t and b lymphocytes defined by t-cell and b-cell receptors (tcrs and bcrs). burnett's "clonal selection theory" proposed that each t and b cell carried a unique receptor specificity, but we now know that any one receptor is capable of recognising multiple epitopes (tcr "degeneracy" and bcr cross-reactivity). any vaccine must therefore contain antigenic epitopes capable of being processed and presented to tcrs, or recognised conformationally by bcrs, and the aim of the vaccine is simply to be recognised by relevant antigen-specific lymphocytes such that these cells are stimulated to generate active immunity and immunological memory. it is therefore irrelevant how large or small the target animal might be; the vaccine simply needs to be able to activate the correct cells in the immunological repertoire. vaccines are formulated with a sufficiency of antigen to achieve that aim. having said that, there is some evidence that dogs of low bodyweight do tend to make higher serological responses to some antigens (kennedy et al. 2007 ) and do have a higher incidence of post-vaccinal adverse events than larger dogs [eb1]. however, at this time, there is no suggestion that vaccines will be formulated on the basis of bodyweight. in north america, some vaccines are available in 0.5 ml rather than 1.0 ml volumes, but the antigenic content of these products is similar. you should never split a vaccine dose between animals or administer anything less than a full dose of vaccine to an animal. this is "off label" use of the product and you would be liable if that animal subsequently developed infection post vaccination. in the 21st century vaccination is no longer simply about inducing protection from infectious disease. therapeutic "vaccines" are used to stimulate or modulate immune responses in cancer (e.g. use of the canine melanoma vaccine) or allergy (use of allergenspecific immunotherapy in atopic dermatitis) and in human medicine there is much active research into therapeutic vaccines for autoimmune diseases. the vgg does not consider these alternative uses for vaccination, which are generally the domain of veterinary specialists. our focus is always on vaccines available globally for the prevention of infectious diseases in dogs and cats, and on products that are used widely in first-opinion veterinary practice. the vgg does not recommend the use of a vaccine to prevent dermatophytosis in dogs and cats since there are very few efficacy studies published. although there are reports of success of anti-dermatophyte vaccines in cattle and fur-bearing animals, the response does not appear to be the same in cats, as these vaccines do not protect against challenge infection (deboer & moriello 1994 , deboer et al. 2002 , frymus et al. 2013 . a commercial vaccine consisting of killed m. canis was licensed in the usa for treatment of cats; however, this vaccine did not provide a more rapid cure of an established infection in vaccinated cats compared with unvaccinated controls. the product was withdrawn from the market (frymus et al. 2013) [eb1] . questions about vaccine delivery 21. can i give core vaccination to puppies at 4 weeks of age if they are due to be sold at 6 weeks of age? the first thing to say about this practice is that 6 weeks of age is really too young for puppies to be weaned, removed from their mothers and sold. in europe it is now illegal to sell puppies that are under 8 weeks of age. the veterinary profession in latam should take ownership of this welfare issue and educate dog breeders as to appropriate times for weaning. bringing together litters of puppies aged 4 to 6 weeks at weekend "puppy markets" is also a "recipe for disaster" in terms of infectious disease transmission and it should also be beholden on the veterinary profession to address this welfare issue. if the bitch that has produced the litter was well-vaccinated, it is likely that she will have a high concentration of serum antibodies against core antigens (cdv, cav and cpv2) and that these will transfer to the puppies in colostrum. in such a circumstance it is unlikely that either a 4-week-old or 6-week-old puppy will respond to core vaccination, although the chances of this are improved if high-titre combination cdv and cpv2 vaccines designed for use in young puppies are applied. however, in latam, it is perhaps more likely that the bitch will not have been well vaccinated and it is therefore correct to attempt to provide protection to puppies as early as possible. the most appropriate way to do this would be with a vaccine containing cdv and cpv and designed for use in young puppies as described above. such a product might be administered from 4 weeks of age; however, mlv vaccines should never be given any earlier than then as they may produce infection and malformation in neonatal animals. after 6 weeks of age, puppies may be vaccinated every 2 to 4 weeks (switching to a trivalent cdv, cav and cpv2 vaccine at 8 weeks old). the most important dose of core vaccine is actually that given at 16 weeks of age or older, when all puppies should have lost maternally-derived antibodies and be capable of responding to vaccine. this should be followed by a fourth core vaccination given between 26 and 52 weeks of age (ideally at the earlier end of that range). it is difficult to be absolutely certain that a litter of puppies or kittens did not obtain colostrum; or that certain individuals within the litter did not obtain colostrum. however, if this is suspected, the first advice would be to implement excellent husbandry by providing as clean and isolated an environment as possible. the use of "artificial colostrum" formulated of milk replacer and serum or plasma from a well-vaccinated adult animal might also be considered in the first 24 hours of life. it is known experimentally that colostrum-deprived animals are capable of making an immune response to core vaccine very early in life (chappuis 1998) [eb1]; however, mlv vaccines should never be used any earlier than 4 weeks of age as they may induce infection or developmental defects in the neonatal animal. core vaccination in this situation might start at 4 weeks of age. although in theory, a colostrum-deprived animal should be capable of responding to a single canine core vaccine or a single dose of fpv vaccine (because there is no inhibition from mda), it would be pragmatic to proceed through the recommended wsava protocol for puppies or kittens. even in a colostrumdeprived kitten, at least two doses of fhv1 and fcv vaccine would be recommended. at 4 weeks of age, the use of core cdv and cpv2 vaccine designed for young puppies would be recommended. this depends on the circumstances and the age the puppy is first presented for core vaccination. initial vaccination would ideally be given whilst the puppies were still with the bitch and arranged by the breeder. in europe, for example, where puppies cannot be sold until after 8 weeks of age and where bitches are likely to be well vaccinated, a breeder might arrange for core vaccination at 8 to 9 weeks of age and then responsibility for subsequent vaccines passes to the new owner. in latam, where a puppy might be obtained much earlier in life, core vaccination might begin as early as 4 to 6 weeks of age (see recommendations above). according to wsava guidelines, puppies may receive core vaccines every 2 to 4 weeks, with the final early-life dose of vaccine being given at 16 weeks of age or older. so the actual number of core vaccines will depend on the age of starting and the frequency of administration. a "standard" protocol in north america or europe might involve core vaccination at 8, 12 and 16 weeks of age with a fourth core vaccine at 26 weeks of age. in latam this protocol might be adapted to account for an earlier onset of core vaccination. there are in-practice serological test kits available on the market that can detect the presence of serum antibody to cdv, cav and cpv2. however, these are designed to inform decision making about revaccination of adult dogs, rather than determine the optimum time for vaccination of puppies. it is simply not practical (and has welfare implications) to repeatedly blood sample very young puppies and, more importantly, until 16 weeks of age, it is not possible to discriminate between mda and antibody produced endogenously by the puppy's own immune system in response to vaccination. so, the answer to the question is "no" it is not possible to use these test kits to determine the optimum time for puppy vaccination. however, the test kits could be used to determine the need for a core vaccine given between 26 and 52 weeks of age (according to wsava guidelines). if a puppy is tested at 20 weeks of age (i.e. 4 weeks after receiving the last core vaccine at 16 weeks of age or older) and is seropositive (for cdv, cav and cpv2), then those antibodies must reflect the puppy's own immune response and indicate that immunological protection has been induced. in that circumstance, the puppy would not require another vaccine at 26 to 52 weeks of age and may go straight into the adult revaccination schedule. there is no evidence that transfer of mda is breed associated or related to body size. transfer does depend on husbandry factors such as the bitch herself being a "good mother" and being able to suckle all her puppies in the crucial window of the first 24 hours of life (although some studies suggest that "gut closure" to absorption of mda may occur even earlier than this). however, the level of mda may vary between different bitches, depending on how well they have been vaccinated. concentrations of mda might also vary for the three major vaccinal antigens (cdv, cav and cpv2) for any one bitch. there are, however, some breeds of dog (e.g. rottweilers, dobermanns) that may more likely include genetic "low responders" or "non-responders" to individual vaccine antigens (day et al. 2016) . it is well recognised in north america and europe that certain individual rottweilers are more susceptible to cpv2 infection (houston et al. 1996) , which is suggested to reflect inadequate vaccinal immune responses; however, in one study dogs of this breed responded adequately to vaccination (coyne 2000) . rottweilers also make lesser serological responses to rabies vaccine (kennedy et al. 2007) [eb1] . serological testing might be used to identify non-responder animals and ideally they would not be used for breeding purposes as they would not be able to transfer adequate mda to any puppies. in an ideal world this would be the case, but it is clear that within a large litter, individual puppies must proactively find a teat in order to take in an adequate amount of colostrum within the first 24 hours of life. smaller or weaker puppies within a litter may not be able to achieve this and will therefore have taken in less mda. these animals will be protected from infection for a lesser period of time during early life, but, in contrast, should be capable of making an endogenous immune response to core vaccines earlier than littermates that sucked more successfully and acquired a greater volume of colostrum. there is no evidence that this is the case. adult dogs that receive triennial core revaccination are known to have stable protective antibody titres during each 3-year revaccination cycle and experimental data have shown that puppies appropriately vaccinated in early life (and then never again as adults) maintain a plateau of protective antibody titres against cdv, cav and cpv2 (schultz 2006) [eb1]. there is a wealth of serological data that shows that annual core revaccination of adult dogs is unnecessary and that protective antibody titres are maintained perfectly adequately with triennial (or longer) core revaccination (abdelmagid et al. 2004 , bohm et al. 2004 , mouzin et al. 2004 , gore et al. 2005 , schultz 2006 , larson & schultz 2007 , mitchell et al. 2012 , killey et al. 2018 [eb1]. some veterinarians like to vaccinate breeding bitches just before they are mated, but there is no evidence that this provides higher quality mda than in bitches receiving a standard triennial core revaccination protocol. 28. how can we safely socialise puppies if they are potentially susceptible to infection (because they are in the "window of susceptibility") at the optimum time for socialisation? the window for effectively socialising puppies overlaps with the "window of susceptibility" to infectious disease (i.e. the short period when puppies no longer have sufficient mda to confer full protection against infection, but still have sufficient mda to block the ability of mlv core vaccines to induce an endogenous immune response) (cutler et al. 2017) [eb1] . there is therefore a theoretical risk that engaging puppies in socialisation activity (e.g. attending a puppy class, exposing a puppy to the outdoors) might allow them to acquire infectious disease. this is a dilemma for the veterinarian; however, we must encourage socialisation as behavioural issues are a major factor in the relinquishment of pet dogs later in life. there are certain practical measures that can be taken to minimise risk: (1) holding puppy classes in relatively clean environments, (2) ensuring that all puppy and adult participants are vaccinated and (3) ensuring the puppy receives the full wsava recommended course of core vaccination. one study from the usa monitored puppies attending puppy classes and did not record a single incidence of infection (stepita et al. 2013) [eb1]; so with common sense the risks are small. the worst case scenario might be that a puppy had blocking mda that prevented generation of an endogenous immune response to core vaccine until the vaccination given at 16 weeks of age or older. within days of that core vaccination the puppy will have generated some immunity, with maximal serum antibody titres likely being achieved around 2 weeks post vaccination. of course many puppies will have responded at an earlier age to core vaccination and in latam where the process of core vaccination might begin even earlier, one might expect protection to be conferred at an earlier age. as walking on the street is part of the socialisation process, the answer overlaps with the question above. common sense should prevail and exposure risk should be minimised during early life. for example, taking such a young puppy to a dog area in a park would not be recommended. there is no evidence that delivering a vaccine to an animal during neutering will fail to engender an active immune response. anaesthetic agents per se are not immunosuppressive and the transient stress and inflammation associated with the surgical procedure will not affect the induction of vaccinal immunity [eb4] . the only reason for avoiding vaccination during neutering relates to the possible very rare occurrence of a vaccine-associated type i hypersensitivity reaction, which might potentially involve an unstarved animal vomiting and aspirating during surgery. this has nothing to do with the efficacy of the vaccine in inducing a protective immune response. one study has shown that vaccines administered to kittens during early neutering did not affect the immune response to the vaccines (reese et al. 2008) [eb1]. 31. why should shelter puppies be vaccinated every 2 weeks from 6 weeks of age to 20 weeks of age if it has been shown that puppies may have persistent maternally-derived antibody until 16 weeks of age? shelters are generally high risk environments with high population density of animals of unknown vaccination and infectious disease exposure history. in the case of puppies entering a shelter, the vaccination history of the dam will also generally be unknown. in order to optimise protection for puppies in such an environment, the vgg recommends this core vaccination schedule where it can be afforded by the shelter. the shelter environment is usually distinctly different from that of a breeding establishment and, subsequently, the new home of an individual puppy. no, this is not necessary. these products are formulated with an "overage" of antigen content to allow for the possible loss of some of the product during administration. if in any doubt, you should contact the manufacturer of the vaccine. the immune system is capable of responding to (or actively tolerating) many thousands of different antigens at any one time. the mucocutaneous surfaces of the body are naturally interacting with very large numbers of antigens (e.g. from the microbiome, dietary antigen, inhaled antigen) in a continual process. therefore, immunologically speaking, the delivery of multiple vaccine antigens on one occasion poses no problem to the immune system [eb4] . for multicomponent vaccines, a requirement of licensing is that it be demonstrated that each component is able to induce a protective immune response. manufacturers also often demonstrate "compatibility" of their own product ranges which are licensed to be co-administered [eb2] . for these reasons, there is no immunological sense in staggering vaccine delivery over different weeks. this would necessitate multiple visits by the client and may increase the likelihood of crucial vaccinations being "missed" from the schedule. one piece of practical advice is that where multiple different injections are to be given (e.g. core vaccine with a separate rabies vaccine), that these be given into different subcutaneous sites so that different draining lymph nodes are targeted for immune priming. two studies from the usa counter this, in that they show for both dogs (particularly of low bodyweight) and cats that there is a greater likelihood of adverse reactions post vaccination when increasing numbers of antigens are delivered at any one time (moore et al. , 2007 [eb1]. vaccinating according to wsava guidelines minimises the number of antigens that might be delivered on one practice visit. a fundamental principle of vaccination is that any animal that is clinically ill should not be vaccinated and vaccination should be delayed until the animal has recovered. if a dog has really recovered from a cdv infection, then it will have natural immunity to reinfection; probably better immunity than might be induced by a vaccine. consequently, that dog could be tested and if seropositive would not require cdv revaccination. however, because the cdv antigen is generally mixed with other core vaccinal antigens, that dog will likely receive standard core revaccination in the future. if it is essential to revaccinate a dog recovered from cdv infection, then a period of 4 weeks post recovery should allow immune function to recover. the situation with ehrlichia canis infection is more complex because the disease may have acute and chronic stages and treated dogs may still harbour the infectious agent such that disease can recur following any future stressful event. again, if a dog has been diagnosed and appropriately treated, it should have been clinically normal for at least 4 weeks before any consideration of vaccination is made. in both circumstances, performing a simple haematological and serum biochemical examination might also indicate that an immunological recovery has been made (i.e. normalisation of leucocyte counts and serum gamma globulin concentration). the simple answer is "no." as above (question 34), if a dog has naturally recovered from cdv infection it will have robust natural immunity against reinfection and in reality does not require cdv vaccine (but will likely receive it as part of a multiantigen core vaccine). remember that the viruses in core vaccines are attenuated and therefore incapable of inducing tissue pathology and clinical disease. there is one recent report and some historical cases of post vaccinal cdv encephalitis in puppies (fairley et al. 2015) [eb1], but this is a very rare occurrence. a dog rescued from the street is taken into a house where there are young puppies still undergoing their early life vaccinations. the dog shows signs of cdv infection after a few days in the new home. should the puppies be vaccinated immediately, rather than waiting until their next scheduled vaccination day? it would always be good practice to isolate such a newly introduced adult dog from the puppies wherever possible (until the puppies had completed their core vaccination schedule). remembering that it is impossible to know precisely when each puppy might have a "window of susceptibility", some puppies might already be immune and others not at the time of introduction. if the puppies are within a 2 to 4 week interval between core vaccines, then in this scenario, there is no harm in revaccinating them earlier than the schedule might have otherwise been and then readjusting the schedule up to the vaccine given at 16 weeks of age or older. however, until the 16 week or older vaccine, there is no guarantee of protection in all cases. a dog that has recovered from natural infection with either cdv or cpv2 will have developed robust immune protection and will be seropositive for the relevant virus. this natural immunity is actually even better than the immunity that might be achieved by vaccination. so, while a recovered dog would likely not require vaccination against that particular pathogen, because core vaccines are formulated as a trivalent product, it will still require vaccination to ensure protection against the other two pathogens (e.g. a dog recovered from cdv infection would still require vaccination against cav and cpv2). this depends on the dose of glucocorticoids given. an anti-inflammatory dose (e.g. 0.5 to 1.0 mg/kg of prednisolone) will not impair the ability of the immune system to respond to vaccination. an immunosuppressive dose (e.g. 2 to 4 mg/kg of prednisolone), particularly if combined with other immunosuppressive agents, is designed to impair immune function. consequently, vaccination should not be delivered until at least 4 weeks after the glucocorticoid has been tapered and then stopped [eb4] . the dog should, of course, also be clinically healthy following the cessation of such therapy. although there are no formal studies of the effects of glucocorticotherapy on canine vaccination, there is a study of the effect of ciclosporin treatment on feline vaccinal immune responses. whilst being treated with ciclosporin, cats were able to make adequate protective immune responses to previously seen vaccinal antigens (fpv, fhv1, fcv, felv and rabies), but the drug impaired the immune response to first-time vaccination with fiv vaccine (roberts et al. 2015) [eb1]. dogs receiving powerful immunosuppressive chemotherapeutic drugs should not be vaccinated. these drugs impair immune function by targeting rapidly-dividing immune cells in addition to the target cancer cells. at least 4 weeks should elapse after stopping such therapy before any vaccines are given. the dog should be clinically recovered and ideally a haematological and serum biochemical evaluation would indicate recovery in immune function. although chemotherapeutic drugs will affect immune function (see question 39), they do not ablate the immune system or destroy memory lymphocytes. therefore, there is no need to routinely revaccinate dogs after completing chemotherapy other than in their normal cycle of core or non-core revaccination. a dog finishing chemotherapy could be serologically tested for the presence of protective antibodies against core vaccine antigens if there was any concern over its level of protection. human patients receiving chemotherapy are not revaccinated at the end of their treatment protocols. there is nothing about the process of surgery and administering an anaesthetic agent per se that would interfere with the ability of the immune system to respond to vaccination [eb4] . however, depending on the nature of the surgery, in the post-surgical recovery period dogs may be clinically unwell and receiving a variety of medical treatments. from first principles it makes sense to wait until the dog is clinically healthy and finished post-operative medical treatment before revaccinating. 42. until which age should i vaccinate an elderly dog? should elderly dogs be vaccinated every year with core vaccines because their immune system might not function as well as when they were younger? for core vaccines (cdv, cav and cpv2) there is good evidence that appropriate puppy vaccination induces lifelong protective immunity without regular adult revaccination. there are also studies that show that geriatric dogs (i.e. dogs over 10 years of age) maintain protective levels of antibody against these three core viral antigens and that these antibody levels do not decline with age as part of the phenomenon of "immunosenescence" (hogenesch et al. 2004) [eb1]. in contrast, it is also known that delivering a new vaccine (i.e. one not previously given) to an older dog leads to a less effective primary immune response than might have been made earlier in life (day 2010) [eb1] . therefore, there is no evidence that geriatric dogs require any more frequent core revaccination than younger adults; geriatric dogs can be safely maintained on the standard triennial core revaccination programme. where core revaccination is determined by serological testing (titre testing), the vgg recommends that this might be performed annually (rather than triennially) in geriatric dogs; simply to provide reassurance that revaccination is not required [eb4]. rottweilers are a breed that is well recognised to contain a higher than average frequency of genetic low responders and nonresponders to cpv2 and rabies vaccines. there is no reason to vaccinate rottweilers any more frequently than other breeds of dog. if they are of this genetic type, that means that the lack the immunological ability to ever respond to the particular antigen (e.g. cpv2); that means that no matter how frequently they are vaccinated, they will not respond to vaccination. this situation is one in which serological testing is of practical benefit. test kits will be able to determine whether a rottweiler is seronegative to cpv2 after vaccination (note that this does not apply to rabies). such a dog would therefore be at risk of contracting infection and appropriate measures might be taken to minimise that risk. more importantly, such dogs should not be used for breeding purposes. there is no evidence that any canine breed or breed group requires any specific vaccination protocol. there has been discussion about small breed dogs (see question 18) and whether rottweilers might require a different core vaccination protocol given the possibility of breed-related poor response to cpv2 and rabies vaccines (see questions 25 and 43). related young dogs of the weimaraner breed are susceptible to a complex syndrome involving hypertrophic osteopathy, chronic recurrent infection and serum igg deficiency. there is a suggestion that onset of this clinical syndrome might be influenced by vaccination (harrus et al. 2002) and there has been some discussion about vaccination protocols for dogs of this breed. however, overall there is insufficient evidence to advise anything except standard core and non-core vaccination, according to guidelines recommendations, for all breeds of dog. if a dog has missed its annual leptospira booster vaccine by a period of up to 3 months, a single "booster" dose of vaccine should be sufficient. if the annual revaccination is delayed by more than 3 months (i.e. a 15-month interval since the last vaccine) then two doses of vaccine (given 2 to 4 weeks apart) should be given to re-establish immunity and then annual boosters thereafter. some manufacturers may advise that protection may extend to 18 months before a new primary course of vaccination is required, but the vgg adopts a more cautious outlook when considering all vaccines in a generic fashion. yes, vaccination will lead to generation of an antibody response post vaccination; however, this may not persist for very long and post vaccinal titres may decline or even disappear by 4 months post vaccination, even though the dog remains protected for the full 12 months cover of the vaccine. although post vaccination titres tend to be low, they may persist for more than 4 months at high levels if the dog is exposed to field strains. also, cross-reactivity with non-vaccinal serovars can occur (sykes et al. 2010) [eb1] . because of this, if attempting to confirm a diagnosis of leptospirosis in a clinically ill dog, the timing of any previous vaccination must be considered. this is one of the major reasons why the clinical diagnosis of leptospirosis can only be achieved properly by assessment of mat testing on paired serum samples taken 2 weeks apart. vaccinal antibodies will not show an increased titre, but antibodies against a potentially infecting serovar should show a four-fold elevation in titre. it is important to highlight that dogs can develop titres against serovars not included in vaccines, and sometimes the highest titre is against a non-vaccinal serovar. positive titres to non-vaccinal serovars should be interpreted with caution if a vaccinated dog develops clinical signs consistent with leptospirosis (barr et al. 2005 , martin et al. 2014 [eb1]. a dog at high-risk for leptospirosis might be one that has regular access to water environments where there may be contamination by rodents or farming environments with livestock. even urban dogs may therefore be at risk. in early versions of the wsava global guidelines, the vgg made the recommendation that 6-monthly revaccination against leptospirosis be considered for high-risk dogs. we subsequently removed that recommendation as there was insufficient scientific evidence to support it. therefore, even high-risk dogs require only annual revaccination against leptospirosis. the vgg would always recommend the use of small antigen combination vaccines (e.g. a trivalent or bivalent core vaccine with separate non-core vaccines) in order to have the flexibility to vaccinate individual animals according to wsava guidelines. as described above, such product ranges allow delivery of the minimum essential antigenic components for that individual animal based on a lifestyle assessment of its exposure risk. giving multiple injections of smaller antigen component vaccines is far preferable to giving a single injection of large multicomponent vaccine containing antigens that are not required or not recommended for that animal. this is one of the greatest challenges in latam; ensuring that the small antigen component product ranges available in other markets are brought to latam, in order to allow veterinarians to vaccinate according to wsava guidelines. for core vaccines and rabies vaccine, a single dose of mlv international quality assured vaccine will induce protective immunity in an adult animal. remember that adult animals do not have blocking mda like puppies and kittens. the one exception to this rule might be for adult cats in the case of fhv1 and fcv vaccines, where to be sure of the best response, two doses (2 to 4 weeks apart) might be given. this is easy to achieve where there is access to a trivalent (fpv, fhv1 and fcv) and bivalent (fhv1 and fcv) vaccine, but in latam, where only trivalent products are marketed, this would necessitate giving an additional (unnecessary) fpv vaccine. moreover, serological testing could be used to determine whether an adult dog actually required any vaccination against cdv, cav and cpv2 or whether an adult cat required any vaccination against fpv (note that at the time of writing the feline test is not available in latam). in the case of non-core vaccines, these will all require two doses given 2 to 4 weeks apart, followed by boosters at the recommended interval. in latam, it is far more important to try to increase herd immunity than it is to increase the vaccination load of individual animals. the more dogs and cats that are vaccinated within the population, the more difficult it is for infectious disease to spread within that population. veterinarians must understand that giving a core vaccine to an animal induces protective immunity. there are not degrees of protective immunity. the presence of antibody against core vaccine antigens, no matter what the titre, indicates that the animal has immunological protection and immunological memory and any exposure to the pathogen results in a rapid secondary (memory) immune response. it is simply not possible to make an individual animal more immune by giving more frequent vaccination. in fact, immunologically speaking and from first principles, repeated vaccination above the recommended levels is more likely to induce immunological "tolerance" (failure to respond) than immunological protection [eb4] . therefore, triennial core revaccination according to wsava guidelines is perfectly adequate, even for the most high-risk of dogs. precious vaccine doses would better be used to improve herd immunity than be wasted on an already well protected animal. here, the veterinary professional needs to ask the question "who is making this regulation"? in many countries (including in north america and europe) the lay owners of boarding kennels and catteries make these rules on the basis that historically, that is what they have always done. these well-meaning individuals are not scientifically trained veterinarians and are generally unaware of the scientific advances in veterinary vaccinology over the past decades. it should be up to the veterinary profession to educate this community and assist them with developing regulations that are consistent with modern science. it is generally accepted that adult cats do develop some level of natural resistance against felv infection; therefore, it is considered more important to establish immunity by vaccination of kittens than it is adult cats [eb4] . any kitten that may have an at-risk lifestyle (i.e. indoor-outdoor access, living in a multi-cat environment) might benefit from felv vaccination, especially where that kitten also lives in an area known to have high prevalence of infection (see main text of this document for where this is known in latam). for adult cats, the vgg currently recommends felv revaccination only every 2 or 3 years, rather than annually. that should be continued lifelong. no. in-practice diagnostic tests for felv detect viral antigen. so a true positive result indicates that the cat is currently infected with felv or fighting off a recent infection. some cats successfully rid themselves of felv. others become persistently or progressively infected. so the cat that tests positive should be retested immediately using a test from a different manufacturer to rule out a false positive result. if a second positive result is obtained, the cat should be retested in 4 to 6 months' time. if the cat remains positive 4 to 6 months later, progressive infection is likely. it is important to highlight that negative antigen tests can occur in infected cats without viraemia, which means that sometimes you may be vaccinating an asymptomatic but felv-infected cat. in this case the vaccine will not cause any harm, but is also unlikely to confer any benefit to the cat. the risk factors for felv infection include outdoor access and exposure to other cats where virus might be transmitted via salivary secretions (e.g. licking, mutual grooming, shared food and water bowls, or biting as part of fighting behaviour). an indoor only cat that may only leave the indoor environment for an annual veterinary visit would not be a candidate for non-core vaccination, including against felv. of course, considering that felv vaccination is most effectively used in kittens, making this decision about the predicted future lifestyle of the cat is sometimes difficult for the owners. if there is any suggestion that the cat might have outdoor access during its future lifetime, or that it will live with other cats that have outdoor access, there is sense in considering felv vaccination in early life; particularly in areas of high prevalence of the infection. ideally, the known felv-infected cat would be housed indoors in isolation and the owners should be advised against introducing any other cat to the household. however, in the situation described, if unavoidable, the new kitten should certainly be vaccinated against felv as soon as possible and ideally before introduction into the household. standard kitten felv vaccination with two doses given 2 to 4 weeks apart beginning at 8 weeks of age and then a 12-month booster is required. ideally, pregnant animals should not be vaccinated. in the case of core vaccines where transfer of mda is required, normally vaccinated adult dams should have adequate titres of antibody for transfer and it should not even be necessary to revaccinate immediately before the dam becomes pregnant. unless indicated specifically by the manufacturer that vaccination is safe during pregnancy (and some products do carry this claim), there are also theoretical risks to the foetus with respect to the use of mlv vaccines in the pregnant animal. non-core vaccines should also not be given during pregnancy; non-core vaccines tend not to induce protective antibody transferred in colostrum in that way that occurs with core vaccines. there is absolutely no evidence to support this procedure even though it remains widely practiced. there is a risk that alcohol may inactivate a proportion of mlv virus particles in a vaccine and so such swabbing is actually contraindicated. although the skin carries a normal microflora, needle injection is highly unlikely to result in any subcutaneous infection by "carriage" of organisms into the skin microenvironment. you should also note that in human medicine, sites of injectable vaccine delivery are no longer alcohol swabbed, according to who and cdc recommendations (e.g. who best practices for injections and related procedures toolkit; accessible on-line) [eb1]. there is no harm in lightly warming a dose of vaccine (i.e. by holding it in the hand) immediately before use, but this is really not required. one study of feline injection site sarcoma suggested that delivery of cold vaccine may be a risk factor for the tumour (kass et al. 2003) [eb1]. however, vaccines should never be over-warmed or kept at room temperature for more than 1 hour. this is because some of the viral components of mlv vaccines are thermo-intolerant and the efficacy of the vaccine will be impaired by warming. vaccines should never be reconstituted early in the morning for use throughout the day. vaccines should always be stored appropriately (refer to table 3 ). for mlv vaccines even 1 to 2 hours at room temperature (and room temperature may fluctuate widely depending on geographical region and season) is sufficient to begin to inactive some of the virus components of the vaccine. more problematic to the veterinary practice is when there may be a power cut and the vaccine refrigerator may be without power for prolonged periods of time. in this context, the recommendation would always be to contact the manufacturer of the vaccines to ask for advice. recent studies suggest that international killed rabies vaccines may actually be quite thermotolerant, but these studies are done against the background of mass vaccination in the field and not from the perspective of practicing quality veterinary medicine in the veterinary clinic (lankester et al. 2016) [eb1]. this is a commonly-held belief that is perpetuated in many parts of the world. virtually all puppies and kittens are born with endoparasites and current recommendations are that regular deworming starts at 2 weeks of age in puppies and 3 weeks of age in kittens (e.g. esccap guidelines; https://www.esccap.org/guidelines/), which is naturally earlier than the administration of core vaccines (from 4 to 6 weeks of age). however, if a puppy or kitten is presented for vaccination, but clearly carries a massive parasite burden to the extent of being severely anaemic and clinically ill, then of course vaccination might best be delayed until the animal is healthy. however, most parasitized puppies and kittens remain apparently healthy. there is currently no evidence to suggest that carrying a "normal" burden of parasites interferes with the ability of a puppy (or kitten) to respond to vaccination. in fact, it may be more important to provide protection against life-threatening viral disease than to worry about any possible effect of parasitism on vaccination. however, immunologically speaking, there is now much research that shows that parasite infestation can influence the nature of immune responses by skewing immunity towards a t regulatory response associated with immunological suppression and a t helper 2 type response dominated by humoral rather than cell-mediated immunity and this has also been shown for the dog (junginger et al. 2017) [eb1] . there are experimental studies in mice and pigs that show that endoparasitism impairs vaccinal immune responses (urban et al. 2007) [eb1] , but what is currently lacking is any evidence that endoparasite infestation impairs canine or feline vaccinal immune responses. deworming is clearly an important part of preventive health care for dogs and cats (and has public health implications), but there is currently no basis for delaying vaccination for susceptible animals until deworming has been completed. any veterinarian who practices in a rabies endemic country, who deals with animals that may be imported from rabies endemic countries or who deals with wild animals (particularly bats) should be routinely vaccinated against rabies according to current recommendations for people. rabies is a fatal disease and no veterinarian at risk of exposure should be unprotected. from the perspective of companion animal practice, there are no other zoonotic diseases for which human vaccination is available or recommended. this relates to what is now known as "vaccination hesitancy" and is of increasing concern in both human and veterinary medicine throughout the world. active lobby groups with strong internet presence promote a culture of fear related to the potential adverse events associated with vaccination of children and pets. the tragedy in human medicine is that such activity has seen a decline in herd immunity for common childhood diseases in recent years, with outbreaks and deaths of once-controlled diseases such as measles. there is no doubt that veterinarians are now also regularly confronted by clients who will refuse vaccination for their pets. it is our professional responsibility to calmly explain the rationale for vaccination, the importance of individual and herd immunity, and the safety of vaccines with very low prevalence of adverse events. this is one reason why the vgg has produced a companion document to the global veterinary guidelines, written in lay language for the pet owner and breeder (unfortunately only in english). this is a factual source of information to which clients concerned about vaccines might be directed. at the time of writing, the vgg is also conducting a global survey of vaccination hesitancy in small companion animal practice. the results of the survey will be presented during 2020. a wide range of adverse events has been recognised post vaccination. most of these are transient and mild (e.g. type i hypersensitivity reactions immediately post vaccination), but some may induce more severe disease (e.g. immune-mediated haemolytic anaemia, feline injection site sarcoma). the single most common "reaction" is mild lethargy, anorexia and pyrexia for 2 to 3 days post vaccination. this is actually not an adverse reaction, but more an indication that the vaccine has stimulated immune and inflammatory pathways as part of generating the protective immune response. it is difficult to obtain accurate data on the frequency of adverse reactions post vaccination. reviewing all of the global information, we can say that there are somewhere between 30 and 50 adverse reactions (mostly mild and transient) for every 10,000 vaccinations given in practice , miyaji et al. 2012 [eb1]. the risk of contracting life-threatening infectious disease (particularly in environments such as in latam) far outweighs the risk of adverse events. theoretically, if a reaction was due to an ige-mediated type i hypersensitivity reaction, the animal is immunologically sensitised and is likely to be affected by the same type of reaction on subsequent exposure to the same antigen. in reality, this does not always happen and sometimes such reactions occur only once. if the reaction has occurred in a puppy or kitten that has not yet received the full course of early life vaccines, then that animal must be revaccinated in order to receive the full schedule of core vaccines. you might consider whether non-core vaccines are justified for that animal, and as an adult, serological testing might be used to inform the need for core vaccines. there are certain practical measures that might be taken to avoid the occurrence of such reactions for second or subsequent times. switching brand of vaccine may or may not have an effect. there is no harm in giving a dose of antihistamine or anti-inflammatory dose of glucocorticoid immediately before vaccination; this will not interfere with the efficacy of the vaccine. the animal may best be kept in the clinic and monitored for several hours post vaccination, rather than being sent home. yes, glucocorticoid at an anti-inflammatory dose may be used, as may a dose of antihistamine. there is no guarantee that this will prevent the reaction occurring again, but there should be no interference with the efficacy of the vaccine. 66. if a dog has recovered from an immune-mediated disease that may have been triggered by vaccination; how should i revaccinate it in the future? immune-mediated or autoimmune diseases are complex multifactorial disorders involving triggering factors acting on a background of immune dysregulation in a genetically susceptible individual. recognised trigger factors for canine immune-mediated diseases include underlying infection, neoplasia, chronic inflammation or recent exposure to drugs or vaccines. the evidence for vaccine-associated autoimmunity in the dog is limited and restricted to clinical observations of immune-mediated disease beginning 2 to 4 weeks post vaccination in the absence of any other possible triggers. the most common disorder linked to vaccination is immune-mediated haemolytic anaemia (imha) with conflicting evidence related to immune-mediated thrombocytopenia (imtp) or immune-mediated polyarthritis. that said, because vaccination is a potential trigger, and because immune-mediated diseases have a relapsing and remitting pattern, careful consideration should be given to revaccination protocols for any dog that has been successfully treated and recovered from an immune-mediated disorder. core revaccination might be avoided if the dog is serologically tested and shown to already have immunity. non-core vaccines should be carefully selected, weighing the balance between disease exposure risk and risk of relapse of immune-mediated disease. it may not be possible (legally) to avoid rabies revaccination; however, in some us states it is possible for the veterinarian to authorise "medical exemption" from rabies revaccination. although these precautions are sensible (from first principles), two recent studies actually show no significant ill-effect when dogs recovered from imha or imtp were revaccinated (ellis et al. 2016b , moon & veir 2019 [eb1]. vaccines are just one of a long list of injectable products that have been associated with fiss. there is something unique about cat (versus dog) subcutis, which means that repeated injection (of anything) may establish a state of chronic inflammation that might at some point transform into neoplastic disease. the cat, in general, appears more susceptible to developing sarcomas following localised trauma or chronic inflammation (morrison 2012) [eb1]. whether adjuvant in vaccines makes vaccines any more likely to induce this reaction is a contentious debate. there is no doubt that adjuvant induces a long-lasting localised chronic inflammatory reaction at the injection site (much more so than non-adjuvanted vaccines) (day et al. 2007) [eb1], but it is suggested that any vaccine is capable of inducing this reaction. in practical terms, the advice is to minimise the use of all vaccines in cats (i.e. by vaccinating according to wsava guidelines) and wherever possible to minimise the use of adjuvanted vaccine as a precaution. consideration should also be given to the site of administration of vaccines to cats (see question 68). there is no specific anatomical location in which a cat might be injected that will reduce the risk of sarcoma developing. however, there are strategies that might be adopted that will aid in the management of sarcoma, should it occur. there are several different options recommended by different organisations and authors. these include administration as far distal as possible subcutaneously into the hindlimbs and forelimbs, administration into the skin of the lateral abdomen and administration as far distal as possible into the tail. the wsava does not recommend a single option, but suggests that at very least the scruff of the neck is not used and that vaccination sites may be rotated each time and that those sites be recorded in the animal's medical record. yes, the vgg is supportive of the use of in-practice serological testing to determine whether adult dogs are protected (i.e. have serum antibody) against cdv, cav and cvp2, and whether adult cats are protected against fpv (at the time of writing the feline test is not available in latam). note that serology cannot predict protection against fhv1 or fcv, or against any non-core vaccine antigens. serological testing for the efficacy of rabies vaccination is often required for the purposes of pet travel, but in this instance, testing is generally performed within a defined period post vaccination (e.g. 4 weeks) and serological testing is not used in general practice to demonstrate protection from rabies because titres can decline after the recommended testing interval. you should select a well-validated test kit supported by peer-reviewed scientific literature. serology might be performed annually or triennially during the annual health check consultation. many owners, particularly those concerned about the safety of vaccines (see question 62) will prefer this option for their pets. yes, one manufacturer makes an in-house test kit to measure fpv, fhv1 and fcv antibodies in the serum of cats (mende et al. 2014 ), but at the time of writing this test is not available in latam [eb1] . note that only antibody against fpv is predictive of protection; antibody against the upper respiratory tract viruses does not correlate with protection. feline vaccine-associated sarcomagenesis: is there an inflammation-independent role for aluminium? veterinary and comparative oncology evaluation of the efficacy and duration of immunity of a canine combination vaccine against virulent parvovirus, infectious canine hepatitis virus, and distemper virus experimental challenges urban domestic dog populations as a source of canine distemper virus for wild carnivores in the coquimbo region of chile epidemiology of canine distemper and canine parvovirus in domestic dogs in urban and rural areas of the araucanıa region in chile high local genetic diversity of canine parvovirus from ecuador prevalence of feline leukemia virus infection in domestic cats in rio de janeiro identification of enteric viruses circulating in a dog population with low vaccine coverage impact of giardia vaccination on asymptomatic giardia infections in dogs at a research facility prevalence of antibodies against three species of leishmania (l. mexicana, l. braziliensis, l. infantum) and possible associated factors in dogs from mérida canine leishmaniosis -new concepts and insights on an expanding zoonosis: part one serologic responses of dogs given a commercial vaccine against leptospira interrogans serovar pomona and leptospira kirschneri serovar grippotyphosa feline panleukopenia: a re-emergent disease correlation between clinical signs of feline conjunctivitis and molecular detection of felid herpesvirus-1, feline calicivirus, chlamydophila felis and mycoplasma felis in cats from shelters in rio de janeiro reliability of techniques used in the diagnosis of canine visceral leishmaniasis by the national control program in brazil: a survey in an area of recent transmission developing practical recommendations for preventative healthcare consultations involving dogs and cats using a dephi technique antibody response to feline panleukopenia virus vaccination in cats with asymptomatic retrovirus infections: a pilot study prevalence of and factors associated with feline leukemia virus (felv) and feline immunodeficiency virus (fiv) in cats of the state of santa catarina seroprevalence of viral infections in domestic cats in costa rica serum antibody titres to canine parvovirus, adenovirus and distemper virus in dogs in the uk which had not been vaccinated for at least three years vaccination with liesp/qa-21 (canileish®) reduces the intensity of infection in phlebotomus perniciosus fed on leishmania infantum infected dogs: a preliminary xenodiagnosis study genotyping of canine distemper virus strains circulating in brazil from detection of feline immunodeficiency provirus in domestic cats by polymerase chain reaction detection by rt-pcr and genetic characterization of canine distemper virus from vaccinated and non-vaccinated dogs in argentina evolution of canine parvovirus in argentina between years 2003 and 2010: cpv2c has become the predominant variant affecting the domestic dog population resurgence of canine parvovirus 2a strain in the domestic dog population from argentina pathologic and immunohistochemical findings of domestic cats with feline panleukopenia feline immunodeficiency virus subtype b in domestic cats in minas gerais, brazil. veterinary research communications neonatal immunity and immunisation in early age: lessons from veterinary medicine occurrence of feline leukemia virus in felis cattus in belo horizonte veterinary dermatology in brazil foco de leishmaniasis en el hobo, municipio del carmen de bolívar molecular and serological surveys of canine distemper virus: a meta-analysis of cross-sectional studies efficacy of two canine parvovirus vaccines for inducing seroconversion in rottweiler and doberman pinscher pups with various levels of maternally derived antibodies feline leukaemia virus associated with leukaemia in cats in santa catarina feline lymphoma and a high correlation with feline leukaemia virus infection in brazil a canine leishmaniasis pilot survey in an emerging focus of visceral leishmaniasis puppy socialization practices of a sample of dog owners from across canada and the united states immunohistochemical detection of antigens of distemper, adenovirus and parainfluenza viruses in domestic dogs with pneumonia ageing, immunosenescence and inflammageing in the dog and cat a kinetic study of histopathological changes in the subcutis of cats injected with non-adjuvanted and adjuvanted multi-component vaccines recommendations on vaccination for asian small animal practitioners: a report of the wsava vaccination guidelines group guidelines for the vaccination of dogs and cats canine coronavirus (ccov) in dogs vaccinated and unvaccinated domiciliated in pelotas, rs, brazil molecular characterization of canine parvovirus variants (cpv-2a, cpv-2b, and cpv-2c) based on the vp2 gene in affected domestic dogs in ecuador the immune response to microsporum canis induced by fungal cell wall vaccine. veterinary dermatology 5, 47-55 30 journal of small animal practice • © 2020 world small animal veterinary association safety and immunologic effects after inoculation of inactivated and combined live-inactivated dermatophytosis vaccines in cats fecal immunoglobulin a antibodies in dogs infected or vaccinated with canine coronavirus seroprevalence of parvovirus, adenovirus, coronavirus and canine distemper virus infections in dogs of santa maria dog overpopulation and burden of exposure to canine distemper virus and other pathogens on santa cruz island effects of maternally-derived antibodies on serologic responses to vaccination in kittens prevalence and risk factors for the presence of serum antibodies against canine distemper, canine parvovirus, and canine adenovirus in communities in mainland ecuador prevalence and molecular epidemiology of canine parvovirus 2 in diarrheic dogs in colombia, south america: a possible new cpv-2a is emerging? comparative efficacy of intranasal and oral vaccines against bordetella bronchisepctica in dogs evaluation of the risk of relapse of canine immune-mediated thrombocytopenia after routine vaccination phylogenetic evidence of a new canine distemper virus lineage among domestic dogs in colombia post-vaccinal distemper encephalitis in two border collie cross littermates the burden of the leishmania chagasi/infantum infection in a closed rural focus of visceral leishmaniasis in lara state, west-central venezuela comparison of two commercial vaccines against visceral leishmaniasis in dogs from endemic areas: igg, and subclasses, parasitism, and parasite transmission by xenodiagnosis prevalence of canine visceral leishmaniasis in municipalities of huila, colombia dermatophytosis in cats: abcd guidelines on prevention and management viral diagnostic criteria for feline immunodeficiency virus and feline leukemia virus infections in domestic cats from characterization of parvoviruses from domestic cats in brazil presence of infectious agents and co-infections in diarrheic dogs determined with a real-time polymerase chain reaction-based panel first record of borrelia burgdorferi b31 strain in dermacentor nitens ticks in the northern region of parana (brazil) borrelia burgdorferi sensu lato in humans in a rural area of paraná state occurrence of chlamydophila felis in a cattery in osasco city, são paulo state isolation and characterization of bordetella bronchiseptica strains from canine origin clinical characterization of the canine distemper in two municipalities of havana three-year duration of immunity in dogs following vaccination against canine adenovirus type-1, canine parvovirus, and canine distemper virus three-year duration of immunity in cats following vaccination against feline rhinotracheitis virus, feline calicivirus, and feline panleukopenia virus development of hypertrophic osteodystrophy and antibody response in a litter of vaccinated weimaraner puppies neutralizing antibodies to distemper and parainfluenza viruses in dogs in shelter kennels in the municipalities of novo hamburgo and porto alegre, rs, brazil concomitant canine distemper, infectious canine hepatitis, canine parvoviral enteritis, canine infectious tracheobronchitis, and toxoplasmosis in a puppy canine morbillivirus (canine distemper virus) with concomitant canine adenovirus, canine parvovirus-2, and neospora caninum in puppies: a retrospective immunohistochemical study disseminated melanized fungal infection due to cladosporium halotolerans in a dog coinfected with canine adenovirus-1 and canine parvovirus-2 isolation and identification of feline calicivirus and feline herpesvirus in southern brazil effect of age on immune parameters and the immune response of dogs to vaccines: a cross-sectional study risk factors associated with parvovirus enteritis in dogs: 283 cases (1982-1991) infectious canine hepatitis: 62 cases immunohistochemical aspects of canine infectious hepatitis maternal antibodies interfere with vaccine protection vaccination against feline panleukopenia: implications from a field study in kittens three-year duration of immunity in cats vaccinated with a canarypox-vectored recombinant rabies virus vaccine three-year duration of immunity for feline herpesvirus and calicivirus evaluated in a controlled vaccination-challenge laboratory trial serum survey for antibodies to coronavirus, herpesvirus, calicivirus, and parvovirus in domestics cats from rio grande do sul, brazil zoonotic intestinal helminths interact with the canine immune system by modulating t cell responses and preventing dendritic cell maturation prevention of feline injection-site sarcomas: is there a scientific foundation for vaccine recommendations at this time? veterinary clinics of north america multicenter case-control study of risk factors associated with development of vaccine-associated sarcomas in cats factors influencing the antibody response of dogs vaccinated against rabies long-lived immunity to canine core vaccine antigens in ukdogs as assessed by an in-practice test kit feline immunodeficiency virus and feline leukemia virus: frequency and associated factors in cats in northeastern brazil three-year rabies duration of immunity in dogs following vaccination with a core combination vaccine against canine distemper virus, canine adenovirus type-1, canine parvovirus, and rabies virus thermotolerance of an inactivated rabies vaccine for dogs feline panleukopenia virus, feline herpesvirus-1 and feline calicivirus antibody responses in seronegative specific pathogen-free kittens after parenteral administration of an inactivated fvrcp vaccine or a modified live fvrcp vaccine occurrence of feline immunodeficiency virus infection in cats three-year serologic immunity against canine parvovirus type 2 and canine adenovirus type 2 in dogs vaccinated with a canine combination vaccine a comparative study of protective immunity provided by oral, intranasal and parenteral canine bordetella bronchiseptica vaccines hepatitis infecciosa canina en la ciudad de corrientes. reporte de un caso infectious diseases of dogs and cats on isabela island serologic survey of domestic felids in the petén region of guatemala vaccine effectiveness and use of collar impregnated with insecticide for reducing incidence of leishmania infection in dogs in an endemic region for visceral leishmaniasis leishmania spp. epidemiology of canine leishmaniasis in the yucatan peninsula assessment of risk for diarrhea in young dogs after giardia vaccine administration amplification of the flge gene provides evidence for the existence of a brazilian borreliosis current status and management of canine leishmaniasis in latin america infection by mycoplasma spp., feline immunodeficiency virus and feline leukemia virus in cats from an area endemic for visceral leishmaniasis vaccine-associated leptospira antibodies in client-owned dogs phylodynamics analysis of canine parvovirus in uruguay: evidence of two successive invasions by different variants frequency of the virus of the feline leukemia (felv) in domestic felines (felis catus) semi-domiciliates in the municipalities of pelotas and rio grande evaluation of an in-house dot enzyme-linked immunosorbent assay to detect antibodies against feline panleukopenia virus molecular and serological characterization of the first leptospira santarosai strain isolated from a dog molecular characterization, serotyping, and antibiotic susceptibility profile of leptospira interrogans serovar copenhageni isolates from brazil situación epidemiológica de la leishmaniosis canina en el paraguay (años 2005-2010) canine visceral leishmaniosis in stray dogs of asunción, paraguay duration of serological response to canine parvovirus-type 2, canine distemper virus, canine adenovirus-type 1 and canine parainfluenza virus in client-owned dogs in australia large-scale survey of adverse reactions to canine non-rabies combined vaccines in japan frequency of feline immunodeficiency virus (fiv) in southern aburrá valley, colombia detection of respiratory viruses in shelter dogs maintained under varying environmental conditions vaccination and associated adverse events in dogs previously treated for primary immune-mediated hemolytic anemia adverse events diagnosed within three days of vaccine administration in dogs adverse events after vaccine administration in cats: 2,560 cases feline immunodeficiency virus and feline leukemia virus infection in free-ranging guignas (leopardus guigna) and sympatric domestic cats in human perturbed landscapes on chiloé island inflammation and caner: a comparative view duration of serologic response to five viral antigens in dogs serosurvey of borrelia in dogs, horses, and humans exposed to ticks in a rural settlement of southern brazil viral diagnostic criteria for feline immunodeficiency virus and feline leukemia virus infections in domestic cats from a randomised, double-blind, controlled efficacy trial of the liesp/qa-21 vaccine in naive dogs exposed to two leishmania infantum transmission seasons infectious canine hepatitis in naturally infected dogs: pathological findings and immunohistochemical diagnosis identification of co-infection by rotavirus and parvovirus in dogs with gastroenteritis in mexico seroprevalence of feline leukemia virus, feline immunodeficiency virus and heartworm infection among owned cats in tropical mexico high prevalence of infection with leishmania (kinetoplastea: trypanosomatidae) in dogs in northern colombia first detection of canine parvovirus type 2c in south america prevalence of felv, fiv and feline heartworm in cats from an animal shelter in maracaibo seroprevalence of canine parvovirus in dogs of boyeros municipality prevalence of canine visceral leishmaniasis in the area of influence of the health unit family marín ka'aguy efficacy of an inactivated canine coronavirus vaccine in pups isolation and characterization of canine parvovirus type 2c (cpv-2c) from symptomatic puppies effects of anesthesia and surgery on serologic responses to vaccination in kittens field randomized trial to evaluate the efficacy of the leish-tec® vaccine against canine visceral leishmaniasis in an endemic area of brazil effect of high-dose ciclosporin on the immune response to primary and booster vaccination in immunocompetent cats isolation of leptospira spp. from dogs with clinical suspect of leptospirosis in são paulo (brazil) combined distemper-adenoviral pneumonia in a dog guías para la vacunación de perros (caninos) y gatos (felinos) en perú autochthonous outbreak and expansion of canine visceral leishmaniasis aafp feline vaccination advisory panel report elimination of neglected diseases in latin america and the caribbean: a mapping of selected diseases european consensus statement on leptospirosis in dogs and cats duration of immunity for canine and feline vaccines: a review comparative onset of immunity of oral and intranasal vaccines against challenge with bordetella bronchiseptica dna detection and evaluation of antibodies against chlamydophila felis in domestic cats from the northeast of the state of são paulo canine-based strategies for prevention and control of visceral leishmaniasis in brazil leptospira noguchii and human and animal leptospirosis, southern brazil serofrequency of feline immunodeficiency virus and feline leukemia virus in cats of araçatuba canine parvovirus type 2 vaccine protects against virulent challenge with type 2c virus survey for tick-borne zoonoses in the state of espirito santo, southeastern brazil frequency of cpv infection in vaccinated puppies that attended puppy socialization classes pan-european study on the prevalence of the feline leukaemia virus infection -reported by the european advisory board on cat diseases (abcd europe) serovars of leptospira isolated from dogs and rodents acvim small animal consensus statement on leptospirosis: diagnosis, epidemiology, treatment, and prevention ocorrência do vírus da imunodeficiência felina e do vírus da leucemia felina em gatos domésticos mantidos em abrigos no município de belo horizonte feline immunodeficiency virus in northern ceará infection with parasitic nematodes confounds vaccination efficacy successful strategies implemented towards the elimination of canine rabies in the western hemisphere rabies update for latin america and the caribbean vaccination of dogs with canine parvovirus type 2b (cpv-2b) induces neutralising antibody responses to cpv-2a and cpv-2c the isolation of leptospires from stray dogs in the city of são paulo coexistence of antibodies to tick-borne agents of babesiosis and lyme borreliosis in patients from cotia county, state of são paulo canine visceral leishmaniasis on margarita island isolation of leishmania infantum, zymodeme mon-1 from canine and human visceral leishmaniasis on margarita island, venezuela. memórias do instituto oswaldo cruz 96 epidemiological aspects of human and canine visceral leishmaniasis in venezuela dear colleague, i am sure that you are aware of the wsava vaccination guidelines group (vgg) and the work we have done since 2004 in introducing global recommendations for the vaccination of dogs and cats. in 2016 the vgg starts an exciting new project that focuses on endemic infectious diseases and vaccination in latin america. the vgg will be making a series of fact-finding visits to countries in the region to meet with a spectrum of veterinary professionals (practitioners, industry, academia and governmental) to formulate recommendations for best-practice vaccination of pet dogs and cats in this part of the world.in advance of these visits, the vgg would like to obtain and analyse information on the perceptions of small animal practitioners working in these countries with respect to infectious disease and vaccination of dogs and cats.accordingly, we have prepared the attached short questionnaire and would be very appreciative of your time in completing this to help us in our endeavours. the data will remain confidential to the vgg and would only be published in anonymous and aggregated form.i thank you for your assistance with our work and look forward to meeting you at one of the continuing education events that the vgg will be hosting in latin america during this phase of our work. triennially (every 3 years) less often (>3 years) is rabies vaccination for dogs a legal requirement in your area?yes no at what age do you give the first dose of rabies vaccine to a puppy? __________________________ do you give a second dose of rabies vaccine to a puppy? if so, at what age?____________________. do you recommend revaccinating adult dogs against rabies? if so, how frequently should they be revaccinated? _____________________. do you use other vaccines in addition to the core vaccines (cdv, cav2 and cpv2) in adult dogs? if so, which ones and how frequently do you give them (i.e. annually? more or less often?) _________________________________________________________________________________. approximately what proportion (%) of your feline patients has ever been vaccinated with the core feline vaccines (fpv, fhv and fcv) these wsava vaccination guidelines have been published as submitted to jsap and have been through an abridged peer-review process. key: cord-025998-1qawjquv authors: lara, r.j.; islam, m.s.; yamasaki, s.; neogi, s.b.; nair, g.b. title: aquatic ecosystems, human health, and ecohydrology date: 2012-03-23 journal: treatise on estuarine and coastal science doi: 10.1016/b978-0-12-374711-2.01015-9 sha: doc_id: 25998 cord_uid: 1qawjquv this chapter treats two main topics: the relationship between human health, aquatic ecosystems, and water use; and the necessity of interdisciplinary approaches for the development of water management policies and disease control. main waterborne diseases, mostly affecting developing countries and relevant in terms of water management and changes in land use, such as malaria, schistosomiasis, or cholera, are discussed stressing links to the global water crisis. also, the role of artificial and natural wetlands in influenza epidemics is treated. the effects of increasing water use and scarcity on human health are discussed considering historical and contemporary incidence of diarrheal diseases in european and south asian megacities, relationships between dams and on waterborne diseases in asia and africa, and intensive agriand aquaculture resulting in man-made ecotones, fragmented aquatic ecosystems, and pathogen mutations. it is emphasized that the comprehension of the multiple interactions among changes in environmental settings, land use, and human health requires a new synthesis of ecohydrology, biomedical sciences, and water management for surveillance and control of waterborne diseases in basin-based, transboundary health systems. surveillance systems should monitor changes in water management, ecotones, and hydrological cycles and shifts in, for example, the outbreak timing of strongly seasonal diseases. these indicators would provide criteria for the development of innovative water management policies, combining methods of vector control and the safe creation of water reservoirs, irrigation systems, and wetland habitats. this chapter is not intended to provide an extensive review of water-borne diseases, since there are already excellent examples of these in the literature. rather, the intention is to call atten tion to particular aspects of the principal water-borne diseases and related water management issues. the emphasis is often on controversial aspects which it is hoped will stimulate an open, undogmatic, and fruitful discussion on possibilities and cur rent and future challenges for ecohydrology in relation to human health. ecological integrity is central to health (epstein, 1999) . pollution, disturbed environments, habitat loss, and climate change promote disease emergence in a number of ways. threats to human health arising from man's interaction with aquatic ecosystems can originate from multiple factors, which can be broadly grouped into the following major categories: • natural biological cycles in which humans can act as hosts of pathogenic microorganisms (protozoans, bacteria, etc.); • consequences of the management of aquatic resources (e.g., wetlands drainage or creation, aquaculture, and dam construction); • effects of water pollution (chemical, microbiological, radio active, and thermal) on man and on the physiology of individual organisms; and • the impact of global changes affecting climate and hydrolo gical cycles (e.g., habitat degradation, warming, increased rainfall, and storms). clearly, these are interlinked and specific case studies are likely to present evidence of more than one causal factor. thus, an effort has been made to integrate these different topics into sections covering the most relevant factors related to diseases that can be considered indicators of determined hydrological processes. globally, approximately 19% of deaths due to infectious dis eases are water related. this amounts to 3.4 million deaths per year, 75% of which are caused by diarrhea, a disease killing around 2 million people every year, mostly children in devel oping countries (wwd, 2001) . thus, it is crucial to develop an integrated water and health management system, as well as the tools required to identify and predict interconnected trends in the evolution of aquatic ecosystems and diseases. although the importance of integrating natural sciences with socioeconomic research is stressed and recommended in every forum dealing with sustainable use of natural resources, human health, one of the most valuable public goods, is seldom included as a significant issue in coastal or basin management programs. a frequent goal of cooperation between socioeconomic and natural sciences research is the evaluation of the sustainability of resource use and the vulnerability of the coastal zone. the seven step assessment framework of the international panel on climate change (ipcc, 1994) is the customary tool used for this purpose (figure 1) . similarly, the health map program from the world health organization (who) provides criteria and a software platform for linking epidemiological data with layers of geographic information (who and unicef, 1993) . however, these two types of research programs mostly lack any substantial interaction. ecohydrology can provide the conceptual framework for establishing such links. this involves a scale (the river basin and the coastal zone), an integrative process (flooding dynamics), and an integrative tool such as digital elevation models (dem) of the study area (figure 1) . high-resolution topography is essential for data integra tion in low-lying areas. for this purpose, a closer interaction of socioeconomic studies, climate, hydrology, ecology, micro biology, biogeochemistry, molecular biology, and medicine is required, as exemplified in the case of cholera (discussed in section 10.12.2.3.1). further, it is necessary to generate a common language to facilitate and promote inter-and transdisciplinary communication. several concepts related to disease dynamics, such as outbreak, epidemics, and pan demics, are commonly used in a qualitative way. yet, the creation of interdisciplinary databanks or the compilation of information from diverse sources (e.g., hydrological events and outbreak intensity) including historical ones would ben efit from objective category definitions. in the following sections, some examples are dealt with, which will appear in this chapter and in other related literature. it is considered that an epidemic occurs when new cases in a given human population, during a given period, sub stantially exceed what is expected, based on recent experience (the number of new cases in the population during a speci fied period of time is called the 'incidence rate'). an epidemic may be restricted to one locality (an outbreak), be more general (the usual 'epidemic'), or even global (pandemic). common diseases that occur at a constant but relatively low rate in the population are said to be 'endemic'. an example of an endemic disease is malaria in some parts of africa, where a large portion of the population is expected to contract malaria at some point in their lifetime. these somewhat subjective definitions require more precisionand a wider diffusion among the populationwhen, for aquatic ecosystems, human health, and ecohydrology 265 figure 1 integration of socioeconomic, ecological, and medical research within the ecohydrology framework. example, public funds have to be allocated for prevention, alleviation, or fight against determined diseases or for insur ance policies. an increasing number of direct or indirect cases of water-borne diseases are due to global warming, increasing frequency and intensity of storms, flood control, and environmental management (dam construction, irriga tion, use of fertilizers, etc.), and this has greatly widened the spectrum of stakeholders with an interest in the use of water and its impact on health. this underlines the need for agree ment on and diffusion of definitions and criteria between users and managers to facilitate the quantification of impacts of disease, ecological damage, and poor sanitation, as well as for cost-benefit analysis of proposed prevention or remedia tion measures. the global burden of disease analysis (who, 2009) pro vides a comprehensive and comparable appraisal of mortality and loss of health due to diseases and injuries, and risk factors for all regions of the world. the overall burden of disease is assessed using the disability-adjusted life year (daly), a timebased measure that combines years of life lost due to premature mortality and years of life lost due to time lived in states of less than full health. worldwide, about 82 million dalys per year are due to water-borne diseases (pruess et al., 2002) . a relevant specific example is the definition and evaluation of the impact of disease related to drinking water quality. this concerns the presence of chemicals or pathogenic microorganisms that are transmitted when contaminated drinking water is directly con sumed. if contaminated drinking water is used in the preparation of food, it can be the source of food-borne disease through consumption of the same microorganisms, often in the form of gastrointestinal illnesses. according to the who (who, 2004a) , diarrheal disease accounts for an estimated 4.1% of the total daly global burden of disease and is respon sible for the deaths of 1.8 million people every year. it is estimated that 88% of that burden is attributable to unsafe water supply, sanitation, and hygiene. at the national level, surveillance systems are the primary source of data concerning the scope and effects of water-borne diseases on persons. these data can be organized to provide information for political and administrative units such as counties or federal states, and/or geomorphological units, that is, basins. in the united states, since 1971, the centers of disease control and prevention (cdc), environmental protection agency, and the council of state and territorial epidemiologists have maintained a collaborative surveillance system which monitors the occurrence and causes of water borne-disease outbreaks (wbdos) (calderon et al., 2002 ). the surveillance system includes data for outbreaks associated with drinking water and recreational water. state, territorial, and local public health departments are primarily responsible for detecting and investigating wbdos and voluntarily reporting them to cdc on a standard form. the unit of analysis for the wbdo surveillance system is an outbreak, not an individual case of a water-borne disease. two criteria must be met for an event to be defined as a wbdo. first, more than two persons must have experienced a similar illness after either ingestion of drinking water or exposure to water encountered in recreational or occupational settings. this cri terion is waived for single cases of laboratory-confirmed primary amebic meningoencephalitis and for single cases of chemical poisoning if water-quality data indicate contamina tion by the chemical. second, epidemiologic evidence must implicate water as the probable source of the illness. the integration of national information on water-borne disease incidence into collaborative regional, transboundary basin databank networks of open access is crucial to allow a fair and efficient implementation of water management regula tions related to, for example, dam operation and international irrigation agreements. this is particularly relevant in tropical countries where large river basins (e.g., amazon, nile, mekong, indus, ganges, and yarlong-brahmaputra) represent the main source of income, water, and food for millions of people. the rivers originating in the tibetan plateau ( figure 2 ) are particu larly relevant as they flow through several, densely populated tropical and subtropical countries with quite different degrees of development. in general, water-borne disease can be caused by protozoa, viruses, or bacteria, many of which are intestinal parasites. in the following tables, some relevant examples of various disease types are grouped and summarized, including those which mostly affect developing countries, in many cases in tropical and subtropical regions. in the following sections, diseases have been selected that are relevant in terms of numerical incidence, water management, and changes in land use, parti cularly under the ecohydrological approach. these are malaria, schistosomiasis, lymphatic filariasis, onchocerciasis, cholera, spotted fever, and those illnesses induced by toxins produced during cyanobacteria blooms due to increased nutrient loads. we will provide a general overview of these diseases, stressing the links to the global water crisis, possible contributions of ecohydrology, and challenges to its classical approach. parasitic infections, particularly malaria and schistosomiasis, represent some of the most universal health problems. the who estimates that 200 million people are infected and another 600 million people are at risk of infection (who, 2007) . in fact, only malaria accounts for more cases of disease than schis tosomiasis, and both are closely related to water management (who, 1993) and will be extensively treated in this chapter. water scarcity and uncoordinated water management go hand in hand with poverty and disease. russel (1961) explains the links clearly: bilharziasis and malaria are both debilitating diseases and debility is not conducive to good farming. throughout history, malaria and bilharziasis have interfered with the use of arid land and indeed, calcified eggs of bilharzia worms were found in the kidneys of two mummies of the 20th dynasty -1250-1000 b.c. there is a crucial chain reaction that in some instances has contributed to the virtual abandonment of irrigation systems: the more debility, the less canal maintenance, therefore the more anopheles mosquitoes and the more snails transmitting more malaria and more bilharziasis, thus leading to more debility, and so on…. (russel, 1961: 253) . table 1 provides a summary of relevant water-borne diseases produced by protozoan parasites. in this section, we will con centrate on malaria, currently still the world's most important parasitic disease. today, malaria is one of the world's deadliest diseases and occurs mostly in tropical and subtropical countries, being transmitted from one person to another through the bite of female anopheles mosquitoes. the who estimates that there are 300-500 million cases of malaria, with over 1 million deaths each year (who, 2001a) . t he main burden of malaria (more than 90%) is in africa, south of the sahara. two-thirds of the remaining burden affects six countries: brazil, colombia, india, solomon islands, sri lanka, and vietnam. the ecology of the disease is closely associated with the availability of water, as the larval stage of mosquitoes develops in different kinds of water bodies. the mosquito species vary considerably in their water-ecological require ments (sunlit or shaded, with or without aquatic vegetation, stagnant or slowly streaming, and fresh or brackish; discussed in section 10.12.4.3.2.1), and this, to a great extent, determines the ecology of the disease. in many places, the nat ural habitat sustains intense malaria transmission; in others, the development of water resources (irrigation, dams, and urban water supply) has exacerbated the intensity of transmission and caused the disease to spread. in yet others, for example, the central asian republics of the commonwealth of independent states, malaria has returned as a result of a breakdown in water management and maintenance problems of local irrigation systems (who, 1999) . climate change (global warming) appears to be moving the altitudinal limits of malaria to higher elevations, for example, in the east african highlands and madagascar. further, in some of the tropical regions of the developing world, the incidence of malaria has increased in recent years as the mosquito and the malaria parasite it transmits have evolved more resistance to sewage, nontreated drinking water, flies in water supply (hand-to-mouth) untreated water, poor disinfection, pipe leaks, groundwater pollution, sharing of water source by humans and wildlife. beavers and muskrats create ponds that act as reservoirs for giardia (oral-fecal, hand-to-mouth) encephalitozoon intestinalis has been detected in groundwater chills, period fever attacks; debility, spleen and liver enlargement; anemia, jaundice; clogging of brain vessels can lead to death flu-like symptoms, watery diarrhea, loss of appetite, substantial loss of weight, bloating, increased gas, and nausea abdominal pain, fatigue, weight loss, diarrhea, bloating, and fever diarrhea, bloating abdominal discomfort, and flatulence diarrhea and wasting in immunocompromised individuals alternatives to dichlorodiphenyltrichloroethane (ddt) and to the medications used to prevent or treat the disease. in some regions (e.g., south africa), ddt is again increasingly used to control mosquitoes (thurow, 2001) . in general, land reclama tion for agriculture, deforestation, and changes in land use are probably the principal causes of the climatic and habitat changes responsible for these developments. yet, it should be borne in mind that it was the drainage of wetlands for agricul tural purposes in the nineteenth century which contributed most significantly to the eradication of malaria in europe (reiter, 2000) . these are crucial aspects to be carefully evaluated when wetland creation and management policy are being considered as an ecohydrological tool, for example, for sequestration of nutri ents in estuaries and for preventing toxic algal blooms. these issues will be discussed extensively in the following section (also discussed in section 10.12.5.2). it is often erroneously thought that larvae of malariatransmitting mosquitoes can only develop in freshwater. it is also frequently forgotten that malaria is not restricted to the tropics, and that only in 1975 did the who declare that europe was free of malaria. about 200 years ago, malaria was a leading cause of death in many marshland commu nities along the coast of southern england. there, extensive salt marshes provided high-quality grazing for sheep and cattle, but were also a favored habitat for anopheles atroparvus, a highly effective malaria vector, which prefers to breed in brackish water along river estuaries and in the presence of abundant algae. until the nineteenth century, malaria was a major mortality factor in the netherlands. however, by the end of that century transmission had dropped precipitously in the more prosperous countries of north europe. a major factor contributing to this decline was that the mosquito habitat had been eliminated by improved drainage and extensive land reclamation. major epidemics still occurred in russia and poland in the 1920s, with high death rates reaching regions near the arctic circle (wolanski et al., 2004 and references therein) . today, malaria is again common in many parts of central america, northern south america, tropical and subtropical asia, some mediterranean countries, and many of the republics of the former ussr. this spread of the disease has been attrib uted to, among other factors, forest clearance, irrigation, ecological change, population increase, deterioration of public health services, resistance of mosquitoes to insecticides, and resistance of the malarial parasite to antimalarial drugs (reiter, 2000) . thus, policies on wetland creation or restoration must take account of not only the benefits of the reestablishment of lost ecological services, but also the potential consequences of increased areas of slow-flowing or stagnant waters on disease vector proliferation, particularly under a scenario of increasing temperatures. the related ecohydrological concepts of system robustness and flushing dynamics can make a major contribu tion to the integrated analysis and handling of this issue, seeking equilibrium between the necessary water residence time, for example, efficient nutrient sequestration, and the minimization of mosquito reproduction. the choice cannot be formulated as 'mosquitoes in the basin' or 'toxic algal blooms in the estuary'. there are techniques such as 'runneling' that have been used with varying success to control mosquito proliferation in cre ated or natural wetlands. as mosquitoes can be vectors for several other diseases besides malaria, this will be treated in a separate section (discussed below in section 10.12.4.3.2.2). table 2 provides a summary of relevant water-borne diseases produced by worm infections. in this section, we will concen trate on schistosomiasis, lymphatic filariasis, and river table 2 main water-borne diseases produced by worms blindness because of their strong links to water management measures, such as irrigation and dam operation schemes. schistosomiasis is considered the second most important para sitic infection after malaria in terms of public health and economic impact. it is a chronic debilitating disease that is estimated to affect between 200 and 300 million people in 79 countries. as many as 600 million live in endemic areas. also known as bilharzia, bilharziosis, or snail fever, it is caused by several species of fluke (trematode) of the genus schistosoma. (gryseels et al., 2006; figure 3) . infection with any of the five species of schistosome worms is rarely fatal. although it has a low mortality rate, schistosomiasis is often a chronic illness that can damage internal organs and, in children, impair growth and cognitive development. the urinary form of schis tosomiasis is associated with increased risks for bladder cancer in adults (hodder et al., 2000) . human infections are most common in asia, africa, south america, or the middle east, especially in areas where the water contains numerous fresh water snails, which are intermediate hosts, that is, may carry the parasite. however, trematodes can be found anywhere human waste is used as fertilizer. the disease affects many people in developing countries, particularly children who may acquire the disease by swim ming or playing in infected water, and field workers in arid or semiarid regions where agriculture depends heavily on irrigation. first infection with schistosomiasis usually occurs during the early school years and is a frequent cause of absen teeism. it is not uncommon for 85% of a school's student population to be infected in some highly endemic areas in africa. in addition to its effect on children, schistosomiasis has a major impact on the agricultural workforce and on national economic productivity. in egypt, where 20% of the people are infected, economic losses due to lost work are estimated to exceed $500 million a year (anonymous, 2009a) . development, both planned and unplanned, has resulted in a number of changes in the epidemiology of the disease that threaten to increase its spread and the number of people infected, reduce economic productivity, and compromise development gains. water development schemes, including dam building and irrigation systems, with slow water flows and aquatic vegetation, have created new breeding sites for snails. intensive agriculture has encouraged people to migrate to urban and peri-urban areas that are ill-prepared to meet their needs for sanitation and water. in these areas, snail-infested streams and canals are often the most convenient water sources. new agricultural systems that emphasize irrigation, double cropping, and other intensive cultivation practices have increased farmers' exposure to infection. the emergence or reemergence of schistosomiasis as a result of large-scale hydroprojects has been reported from the egyptian aswan high dam (khalil, 1949; strickland, 1982) , the sudanese gezira-managil dam (amin, 1977; omer, 1978 (teklehaimanot and fletcher, 1990) . in china, the danling dam in the province of sichuan and the huangshi dam in the province of hunan have all had adverse effects by increasing local schistosome transmis sion (zhang and guo, 2006) . however, not all dam regions suffer from schistosomiasis. for example, when the ertan dam in the province of sichuan became operational, local schistoso miasis control centers collaborated with dam management offices and government ministries to actively monitor and pre vent the spreading of schistosome worms. as a result of these efforts, potential schistosome transmissions in the ertan region were successfully averted (gu et al., 2001) . schistosomiasis infection in humans, the definitive hosts, is caused mainly by three species of flatworm, namely schistosoma haematobium, s. japonicum, and s. mansoni. infection occurs when free-swimming larvae penetrate human skin. the larvae develop in freshwater snails, which serve as intermediate hosts for the parasite. humans are infected when they enter larvaeinfested water for domestic, occupational, and recreational purposes and the larvae of the parasite penetrate the unbroken skin. the life cycle is continued when people infected with schistosome worms deposit urine or fecally borne eggs into the water. the disease particularly affects children who may acquire the disease by swimming or playing in infected water (hodder et al., 2000) . the life cycle of s. mansoni provides a simplified example for all species of schistosomes and helps understand the potential contribution of water management to snail proliferation. after the eggs of the human-dwelling parasite are emitted in the feces, into the water, the ripe miracidium hatches out of the egg. the miracidium searches for a suitable freshwater snail to act as an intermediate host and penetrates it. following this, the parasite develops, via a so-called mother-sporocyst and daughter-sporocyst generation, into the cercaria. the purpose of the growth in the snail is the numerical multiplication of the parasite. a single miracidium can produce several thousand cercaria, each one of which is capable of infecting humans. the cercaria propel themselves in water with the aid of their bifurcated tail and actively seek out their final host. when they recognize human skin, they penetrate it within a very short time. following a migration through the body within the bloodstream, they develop into sexually mature adults. the larvae enter through the skin, migrate via the blood vessels, and mature in the lungs. from there they travel to the veins of the upper or lower intestine or bladder and, if they find a partner of the opposite sex, they reproduce. there are specific host/parasite combinations that lead to typical forms of bilhar ziasis in endemic areas in different regions of the world, frequently associated with a particular economic activity. there are also region-specific control measures with positive and negative consequences or side effects (mannesmann and fuchs, 2003) as discussed in section 10.12.2.2.1.1. in these regions, the snail bulinus truncatus, b. globosus, and b. forskali can be hosts of s. haematobium, which produces uro genital bilharziasis (lang, 1996) . the two clearest examples of large-scale irrigation systems spreading schistosomiasis are found in africa, especially in the nile valley. in upper egypt south of cairo, it has been known for a long time that the shift from basin irrigation by the floodwaters of the nile to perennial irrigation results in a dramatic increase in schistosomiasis. basin irrigation allows the land to dry out seasonally, killing almost all snails. under perennial irrigation, the land is wet all year round. soon after the construction of aswan low dam, four locations that changed irrigation methods in the mid-1930s experienced a surge in s. haematobium infections (khalil and abdel azim, 1938; khalil, 1949) . infection rates increased from 2-11% in 1934 to 44-75% in 1937. urinary schistosomiasis had a pre valence at 60% in areas of perennial irrigation in upper egypt and only 5% in areas with basin irrigation (scott, 1937) . in the 1950s, prevalence ranged from 56% to 68% in three districts with perennial irrigation, while in two districts with basin irriga tion, it was 9% and 13% (wright, 1973) . in the 1970s, after the construction of the aswan high dam, the nile delta became a major breeding habitat for the snail hosts of both urinary and intestinal schistosomiasis. irrigation canals and drains ( figure 4 ) harbored stable populations of these snails throughout the year. this resulted from the elimina tion in these canals of the so-called 'winter closure'. before the construction of the dam, the closure was enforced for about 40 days, during which the canals were closed and dried up, and the silt deposited on their beds during the nile flood was dredged out together with the snails and aquatic weeds (malek, 1975) . the other large-scale nile valley irrigation system impli cated in schistosomiasis transmission is the gezira irrigation scheme in the sudan. the major increase in prevalence of schistosomiasis in gezira came after 1960, when the cropping rotation changed to include 'winter' wheat. farmers kept the canals filled with water from march to may, when they were previously dry (fenwick, 1989) . another factor was the creation of the adjoining managil extension irrigation system which left tenants without adequate water supplies or sanitation facilities. also, there was an influx of migrant laborers in the original gezira scheme, who lived near irrigation canals, under very poor sanitary conditions, leading to the propagation of further water-borne diseases (tameim et al., 1985) . in north africa and the middle east, research has demon strated the association of even small-scale irrigation plans, decentralized at the village level, with increases in schistoso miasis transmission. malek (1962) reports that in sudanese villages along the nile, north of khartoum, prevalence of urin ary schistosomiasis in children was 11-12%, compared to an average of less than 2% in other areas. wright (1973) reports that in the rural area around baghdad, iraq, prevalence of schistosomiasis increased from 10% to 25% following the installation of lift pumps. 10.12.2.2.1.2 asia in east and southeast asia, intensification and expansion of irrigated rice production systems over the past decades have increased the habitats for snail and schistosoma. the host/para site combinations tricula aperta/s. mekongi and oncomelania hupensi/s. japonicum produce intestinal bilharziasis predomi nantly in rural communities living close to irrigation ditches. the association of asian schistosomiasis with rice-growing areas has been reported by different authors. however, in many cases, rice fields themselves did not seem to be breeding habitats; rather snails found in the rice fields appeared to have spread from nearby irrigation canals. cattle and water buffalo can also be important reservoir hosts. various methods have been applied to substantially reduce schistosomiasis in rice agriculture, which will be discussed later in section 10.12.4.3.1. in this part of the world, it is mainly the combination of s. mansoni with biomphalaria glabrata snails that causes bilhar ziasis. brazil, with 25 million people living in the endemic areas and 3 million infected, is the most affected country in the americas (chitsulo et al., 2000) . however, it is not obvious to what extent hydrological factors, including large dams or irrigation systems, contribute to spreading schistosomiasis in brazil. the african slave trade was probably responsible for the introduction of schistosomiasis in brazil soon after the country was discovered by european explorers, and internal migration was responsible for spreading it from seashore to interior. nowadays, schistosomiasis transmission occurs over a vast endemic region, from maranhão to espírito santo, and minas gerais, and there are further areas with a high risk of endemic expansion (araujo, 1986; paraense, 1986) . there are also iso lated foci in the federal district and in the states of pará, goiás, rio de janeiro, são paulo, paraná, and rio grande do sul. some examples from the literature point to patterns of labor and household migration as significant factors in the incidence of disease in brazil, probably more than irrigation schemes. cases of disease importation from endemic areas have been registered over almost the entire country, mainly in the states that are considered migration destination areas, such as rondônia (coura and amaral, 2004) . a study involving 23 irrigation projects in the semiarid region of five northeastern states of brazil (coutinho et al., 1992) found that schistoso miasis transmission was not a major problem in the areas studied. socioeconomic-sanitary analysis identified the pre sence of migrant farm workers coming from endemic areas of schistosomiasis and living in poor sanitary conditions in the irrigation areas as a main factor of epidemiological importance. however, continued epidemiological surveillance is essential in all irrigated areas of northeastern brazil if schistosomiasis control is to be maintained, as well as improvement in the water supply and sanitation measures for migrant workers (coutinho et al., 1992) . the potential association between irrigation levels and the occurrence and spread of s. mansoni infection was investigated (martins and barreto, 2003) in the state of bahia, where two forms of irrigation have been developed. the first is capital intensive and mechanized, requiring little manual labor. the second is labor intensive and characterized by limited mechan ization. according to the study, the municipalities with the largest irrigated areas are not the ones with the highest s. mansoni infection rates. in most of these counties, irrigation is capital-and technology intensive. according to these find ings, unlike africa, irrigation in the state of bahia has had little impact on the spatial profile of the schistosomiasis endemism. regarding the impact of schistosomiasis on labor-intensive irrigation schemes, some research points to the importance of the household in disease transmission, as a result of the cluster ing of domestic activities associated with water collection, storage, and usage. such activities can result in the sharing of water-contact sites and water-contact behavior, which expose all members of the household to an increased risk of infection. in previous studies in brazil (bethony et al., 2004) , it was deter mined that shared residence accounted for 28% of the variance in schistosoma fecal egg excretion rates. further, shared residence accounted for 30% of the variation in total water contacts per week. it also accounted for a large proportion of the variation in individual water-contact behavior: for example, agricultural con tacts (63%), washing limbs (56%), or bathing (41%). these results implicate the household as an important composite measure of the complex relationships between socioeconomic, environmental, and behavioral factors that influence water-con tact behavior and, therefore, the transmission of schistosomiasis. these results also support the idea of focusing on safe water supply and household density in the implementation of schis tosomiasis prevention and control measures. the role of aquatic animals in maintaining the schistosome life cycle in brazil requires further clarification. the influence of s. mansoni on a population of the water rat, nectomys squamipes, was studied at sumidouro, rio de janeiro, and brazil (d' andrea et al., 2000) . the population dynamics of parasites was studied. water contamination (i.e., the source of miraci dia), abundance of the intermediate host, and rodent migration were found to be related to schistosome prevalence. the n. squamipes population was not obviously influenced by the infection, as shown by the high number of reproductive infected females, high longevity of infected individuals, and the absence of a relationship between recruitment or survivorship rates and the intensity of schistosome infection. the data indicate that n. squamipes can increase transmission of s. mansoni in endemic areas and carry it to noninfected areas. furthermore, this rodent can be used as an indicator of trans mission foci. in the caribbean, b. glabrata can be found in shallow ponds with abundant vegetation or with fallen banana leaves. it has been also found in drains around banana plantations on the west indian island of st. lucia (sturrock, 1975) . this is a mosquito-borne parasitic worm infection, a debilitating parasitic disease, which affects 170 million people in the tropical and subtropical areas of southeast asia, south america, africa, and the islands of the pacific. while filariasis is rarely fatal, it is the second leading cause of permanent and long-term disability in the world. a person with the disease tends to have more bacterial infections in the skin and lymph system. this causes hardening and thickening of the skin, which in its most dramatic form is expressed in the symptoms of elephantiasis, the accumu lation of lymph, usually in legs. it is not a killer disease, but causes severe debilitation and social stigma. the who has named filariasis one of only six 'potentially eradicable' infectious diseases and has embarked upon a 20-year campaign to eradi cate the disease. in addition to consistent long-term treatment by oral medicines, eradication efforts focus on controlling the pro liferation of mosquitoes in aquatic environments, which will help to reduce the transmission of lymphatic filariasis, as well as that of malaria, which is prevalent in many of the same communities in africa (cdc, 2005) . onchocerciasis or river blindness is the world's second leading infectious cause of blindness. it is found in 36 countries in africa as well as in guatemala, southern mexico, some areas of venezuela, small areas in brazil, colombia, and ecuador, and in the arabian peninsula. a total of 18 million people are affected worldwide. the disease is caused by onchocerca volvulus, a parasitic worm that breeds in water and that can live for up to 14 years in the human body. controlling insect breeding sites in rivers is one of the pillars of prevention. the disease is trans mitted person to person by bite of a blackfly (simulium), which breeds solely in fast-flowing waters. symptoms of the disease in a person usually begin to show 1-3 years after infection. each adult female worm, which can be more than half a meter in length, produces millions of microscopic young worms (micro filaria). the microfilaria migrate through the skin and, upon death, cause intense itching and depigmentation of the skin (leopard skin), lymphadenitis, resulting in hanging groins and elephantiasis of the genitals, serious visual impairment, and blindness when they reach the eye. the disease blinds between 10% and 30% of its victims and seriously undermines the economic productivity of communities in endemic areas (who, 2001b; figure 5 ). figure 5 onchocerciasis also affects the development of exposed children. their school performance is affected by the unrelenting itching associated with this disease. many youth are deprived of their childhood as they are often forced to guide and look after elderly relatives blinded by the disease. photo credit: bill vanderdecker in: http://www.pqmd.org/cms/node/116 unlike malaria and schistosomiasis, transmission of river blindness is usually found along fast rivers or streams with white-water rapids and cascades. the species of blackflies, which transmit this blinding parasite, require well-aerated, high-velocity flow to deposit their eggs, usually on rocks or overhanging vegetation. the larval stages are filter feeders and need large flows passing their habitat to obtain sufficient food and oxygen for development. in many parts of africa, people living near rivers migrate out of the fertile river valleys because of the painful bites of the flies and the eventual blindness resulting from this parasite (kim and merritt, 1990) . river blindness has historically plagued the fertile valleys of west africa, but it was the arrival of europeans that unleashed the full force of the disease upon the region's inhabitants. traditional taboos had kept people from settling along river banks or visiting streams in broad daylight, when blackflies are most active. white colonists, however, insisted on recreating the riverside towns they remembered from home. by removing longstanding cultural prohibitions, they made onchocerciasis more prevalent than it had been before. by the 1970s, several hundred thousand people had been blinded by the disease. also tragically for the region, the most fertile farmlandan area roughly the size of michiganwas abandoned due to the risk of contracting the disease (wong, 2008) . currently, river blindness has been eliminated as a major public health problem in west african countries. despite success in west africa, 109 million people remain at risk of contracting river blindness in the 19 countries of central, eastern, and southern africa (anonymous, 2007) . due to the tight connec tions between the dynamics of this disease and changes in flow velocity, we will return to it in section 10.12.3.3 in the discus sion of the effect of dams on human health. table 3 provides a summary of relevant water-borne diseases produced by bacteria. we will concentrate on cholera and other vibrio illnesses for the reasons explained below. the case of cholera has been considered paradigmatic of the links between global climate change and infectious diseases. it offers an excellent example of how information about environ mental factors permits better understanding of disease virulence, transmission, and epidemiology. therefore, and due to the links to wetlands and other coastal ecosystems, aquaculture, and water management in megacities, this disease will be discussed in detail in this and the following sections, in relation to the dynamics of its causative agent in aquatic ecosystems. cholera is still an important cause of morbidity and mor tality in many countries in asia, africa, and latin america due to lack of safe water supply and poor hygienic practices (colwell, 1996) . cholera is endemic in the ganges and brahmaputra deltas. it was originally endemic to the indian subcontinent but spread worldwide along the trade routes, and mostly affects developing countries, particularly in coastal zones. in the last ∼200 years, there have been seven pandemics and there is evidence of accelerated change of vibrio and disease dynamics as consequence of environmental changes and increased global connectivity (faruque et al., 2003) . the cur rent pandemic, which started in 1961, is the most extensive in geographic spread and duration. cholera epidemics were reported from over 90 countries during 1994, the largest scale ever recorded in human history (who, 1998) . vibrio cholerae, a gram-negative comma-shaped gammapro teobacterium, is the causative agent of cholera ( figure 6 ). vibrios are aquatic bacteria of marine and estuarine origin but can survive and be pathogenic in freshwater ecosystems. apart from v. cholerae, some other vibrios (v. parahaemolyticus, v. vulnificus, etc.) are also responsible for incidences of diarrhea, gastroenteritis, necrotizing fasciitis, and septicemia, which afflict human populations (table 3 ) all over the world (chakraborty et al., 1997) . besides, many vibrios can also cause diseases in fish, shrimp, corals, and other aquatic organisms (thompson et al., 2004) . there are convergent approaches to the investigation of coral and human diseases. these include the research into the figure 6 the causative agent of cholera, vibrio cholerae, is a faculta tively anaerobic bacterium, 0.5-0.8 µm to 1.5-2.5 µm, and a natural inhabitant of temperate/tropical estuaries, salt marshes, mangroves, coastal waters, and reefs. photo credit: moredun animal health, ltd/ science photo library/photo researchers, inc. same bacteria genus (vibrio), responsible for coral bleaching and for cholera, the use of remote sensing of ocean-surface temperature, climate research, and an emerging common cur rent of epidemiological thinking. traditionally, the association between water temperature and coral bleaching has been stressed, and only recently it has been discovered that this is probably triggered by a vibrio bacterium, and that it could be transmitted by a coral-feeding worm, acting as 'vector'. it is the first time a vector has been found for a coral disease (rosenberg and falkovitz, 2004) . table 3 main water-borne illnesses produced by bacteria at the same time, the study of cholera disease has begun to encompass marine and estuarine research. the association of v. cholerae with plankton was established only recently, allow ing analysis of patterns of cholera epidemics, especially in those regions where it is endemic. the sporadic and erratic nature of cholera epidemics can now be related to climate-ocean coupling events, such as el niño (colwell, 1996) . since zoo plankton has been shown to harbor the bacterium and zooplankton blooms follow phytoplankton blooms, remote sensing can be employed to determine the relationship between cases of cholera and ocean chlorophyll concentration, as well as sea-surface temperature, ocean height, nutrient con centrations, salinity, and turbidity. during each pandemic, cholera has struck coastal regions before spreading inland. the principal agents responsible for cholera epidemics are the o1 and o139 serogroups of v. cholerae, of more than 200 serogroups so far identified. within the o1 serogroup, the classical biotype caused the pre vious six pandemics, while the el tor biotype is associated with the present seventh pandemic. a coupling of vibrio dynamics to that of aquatic, brackish ecosystems is strongly suggested by the marked cholera seasonality in coastal villages of the bay of bengal (colwell, 1996) . the role of coastal areas in maintain ing endemicity is clearly a significant feature of cholera ecology. however, it was mainly laboratory research that provided evi dence for the existence of aquatic environmental reservoirs where v. cholerae survives for long periods of time and from which a toxigenic form may emerge to support epidemic con ditions (miller et al., 1984 (miller et al., , 1985 (miller et al., , 1986 barua and greenough, 1992) . the o139 serogroup emerged in the coastal zone in 1992 through a natural genetic alteration of the o1 el tor biotype. a survey in bangladesh established that this strain was mainly found in southern coastal marshes (faruque et al., 2003) . however, systematic, interdisciplinary field studies on the relationship between habitat characteristics and vibrio diversity and virulence are scarce. little has been done to widely monitor v. cholerae and study its ecology from a basin perspec tive in different related coastal environments such as mangroves, marshes, and estuaries, despite clear evidence that this could be one significant step forward for early warning and understanding human vulnerability to the disease (collins, 2003) . as early as 1884, robert koch suggested that the bay of bengal, especially the sundarban mangrove forest, was the main source of cholera, noting that the combination of a brackish, organic-matter-rich environment, with a high den sity of human population represented the ideal conditions for the proliferation of v. cholerae (koch, 1884) . however, since then, there have been no extensive surveys of this transbound ary ecosystem (bangladesh and india), which represents the largest unitary mangrove and marsh system worldwide (akhtaruzzam, 2004) . difficult access, cyclones, floods, and the difficulty of obtaining funding for long-term research have precluded the systematic spatiotemporal monitoring of these habitats. most of the few available works are based on one-site samplings and do not provide information on seasonal trends. plankton is a significant marine reservoir of v. (huq and colwell, 1995) . in most cases, phytoplankton and zooplank ton are spatially and temporally associated (kiorboe and nielsen, 1994) and their abundance can be estimated by remote sensing, which has been related to cholera incidence in the bay of bengal region by lobitz et al. (2000) . living zooplankton can be a reservoir for vibrios, which attach them selves to the zooplankton's chitinaceous exoskeleton (kaneko and colwell, 1975) . nevertheless, watkins and cabelli (1985) found that growth and survival of v. parahaemolyticus was more stimulated by addition of pulverized chitin, than by living zooplankton, which however had a greater effect than the addition of sewage or other nutrients. in addition to salinity, nutrients, and plankton, suspended particle load and sediment resuspension also influence the vibrio amount in the estuary. recent investigations (lara, unpublished results) on seston size fractionation in sunderbans waters showed that the largest amounts of chitin and cultivable vibrio spp. were generally present in the fractions correspond ing to micro-, nanoplankton, microdetritus, and silt/clay particles, and not in zooplankton. it is still an open question whether the vibrio serotypes o1 and o139, as well as the viable but not cultivable, and nonviable forms are preferen tially associated with determined seston size classes or wetland ecosystem compartments. better understanding of vibrio diversity in aquatic environ ments such as estuaries, marshes, and mangroves can lead to new insights into their genetic expression and co-regulation in the environment where they interact with each other. however, most vibrio studies treat species of pathogenic importance (e.g., v. cholerae, v. parahaemolyticus, and v. vulnificus) and not the diversity of the genus itself. a further key issue is the compre hension of the seasonality, life cycle, and dormant phases of bacterial population in nature. the environmental persistence of v. cholerae may be facilitated by entering a dormant state in which it remains viable but becomes nonculturable (vbnc) in conventional laboratory media (colwell et al., 1985) . the v. cholerae cells attached to plankton enter into the vbnc state as survival strategy (colwell and huq, 1994) . therefore, the detection of the nonculturable state is crucial to understanding v. cholerae ecology. however, the mechanisms that cause the organism to associate with plankton or other particles, to form biofilms, or to enter dormant or free-swimming phases are not yet completely understood. in the karnaphuli estuary, bangladesh, recent studies (lara, unpublished) showed that suspended particulate matter (spm) other than zooplankton contained significant amounts of chitin, especially in the size class <20 µm. the quantitative contribution of respectively nano-or bacterioplankton, microdetritus of biological origin, or resuspended sediment particles to the chitin pool in that size class is still unknown. particle load together with salinity significantly influenced estuarine vibrio distribution. we compared the microbial landscape dur ing a pre-monsoon situation and after a strong cyclone: the amount of cultivable vibrio, and its relative contribution to total aerobic bacteria, increased dramatically after the cyclone. amounts of spm also increased and there were higher salinities along the estuary. sediment resuspension and salt intrusion can thus strongly influence the abundance and distribution of estuarine vibrio population. the above findings call attention on essential questions relating estuarine dynamics and human health: are vibrios in sediment part of a benthic community with its own character istics or do they basically consist of a fraction of a pelagic population reaching the sediment after sedimentation of the particles to which they are attached? nair et al. (1988) also addressed the role of sediments as a possible vibrio reservoir in freshwater environments in calcutta. in florida, there was a predominance of non-o1 v. cholerae infections at the time the organisms flourished in the sediment (williams and larock, 1985) , which was detected down to 15-cm depth. higher sedi ment vibrio concentrations were associated with organic matter flocs occurring after the seasonal phytoplankton productivity maximum and during the zooplankton decline. this suggested that the flourishing of vibrio in the sediments was related to the presence of organic matter input from plankton detritus. thus, although plankton itself is an important aquatic vibrio reser voir, its relevance for fueling benthic vibrio seasonal cycles has probably been overlooked. the relevance of seasonally driven sediment resuspension in relation to annual cholera cycles in endemic regions deserves more attention. the incorporation of particle-bound vibrios and porewater nutrients into the water column could favor a sharp vibrio increase, even at otherwise unfavorable salinities (singleton et al., 1982) . future studies should investigate the links between the spatiotemporal estuarine variability and the ecology, diversity, and spreading mechanisms of vibrios including v. cholerae. a key question is how and to what extent these microorganisms persist in the transition from a brackish to a freshwater envir onment, involving strong gradients in salinity, ph, inorganic nutrients, dissolved and particulate organic matter, turbidity, plankton, and wetland vegetation. further, an ecohydrological research approach should focus on how the distribution of the above factors influences the relative abundance of v. cholerae compared to the total vibrio population and other bacterial groups in aquatic environments of west bengal, including water and sediment compartments. there have been efforts to predict cholera outbreaks through models relating disease incidence and environmental variables such as seawater temperature, chlorophyll content, height of the ocean surface, and rainfall, as well as by remote sensing (e.g., lobitz et al., 2000) . recently, an empirical model relating multiyear data of the number of cholera cases, rainfall, and chlorophyll was able to successfully reproduce outbreaks of cholera in kolkata and matlab over the time span of the data set (magny et al., 2008 ). yet, these authors stated that a finer temporal resolution (submonthly) in environmental data col lection was needed to improve mechanistic models and account for short-term variability, especially for the kolkata region. there is also evidence that cholera cases increased following a rise in ocean-surface temperature. however, a direct correla tion exists only for the spring peak, while during the rest of the year there are lags and even an inverse correlation between the two variables (colwell, 1996) . simple (lag) correlations between the seasonality of cholera and that of climate variables such as monsoon rainfall merely confirm that cholera is seaso nal (bouma and pascual, 2001) . these authors hypothesized that there would be two different aquatic habitats: the marineestuary type and the inland water bodies, with potentially different driving factors. although much has been speculated about possible ocean/ land interactions based on empirical correlations, the causal links between ocean parameters and cholera incidence in ripar ian inland villages are tenuous, as discussed in the following. zooplankton in freshwater has been considered a main trans mission means of v. cholerae to humans . although tidal transport of vibrio-carrying marine zooplankton toward the inland is likely and has been proposed by these authors as a possible infection source, until now there have been no studies demonstrating that marine copepods survive long enough to represent an infection source in freshwater, which is what people drink finally, and not seawater. simultaneous variation of two parameters does not imply causality and, although the existing mechanistic models can be useful as predictive tools, they have not significantly contributed to explaining the reasons for cholera endemicity or the existence of bimodal and unimodal occurrence patterns in the indian subcontinent. for example, sea-surface tempera ture in the bay of bengal shows a bimodal cycle similar to the seasonal pattern of cholera in dhaka, bangladesh (colwell, 1996; figure 7) , and is therefore often used, directly or through covarying parameters, with success for such models. however, this seems to mask the fact that strong unimodal patterns are observed elsewhere in india (e.g., north bengal and vellore; jesudason et al., 2000; bouma and pascual, 2001) without any obvious relationship to the marine environment or even to temperature and rainfall. several studies found that the effect of rainfall on cholera incidence does not show any univocal pattern (glass et al., 1982; bouma and pascual, 2001; ruiz-moreno et al., 2007) . even in dhaka, which has a strong bimodal seasonality, there is no clear relationship between rainfall and cholera. the number of cases peaks before the monsoon (high rainfall period) and at its end, with a strong decrease in the middle of the monsoon. recently, hashizume et al. (2008) showed that the weekly number of cholera cases in the period 1996-2002 in dhaka did not show any direct relationship to rainfall, and suggested that river levelbelow flooding levelalso plays a role. river discharge is controlled not only by rainfall but also by snow melting in the himalayas and can control the survival of the bacterium through determining salinity and ph levels (bouma and pascual, 2001) . hashizume et al. (2008) stated that, because of the observed and potential effects of chemical changes in surface waters due to rainfall on vibrio survival and toxicity, it is necessary to quantify the level of v. cholerae in aquatic environments at the same time as measuring rainfall and river levels ( table 4) . this section deals with examples of diseases derived from or influenced by high nutrient loads, particularly those derived from toxic algal blooms, as well as with the general effect of global changes in nutrient cycles on parasitic infectious diseases according to toxin type and exposure: skin irritation, stomach cramps, vomiting, nausea, diarrhea, fever, sore throat, headache, muscle and joint pain, liver damage, and kidney disease in the body nitrate is reduced to nitrite, which reacts with hemoglobin forming methemoglobin, and reducing blood ability to carry oxygen; affects mostly infants and old persons (pids). although arsenicosis affects millions of people, parti cularly in bangladesh, the problem arises from using water from wells reaching layers where groundwater naturally con tains high as levels and there is, to date, no obvious way that ecohydrological methods could help solve this problem. for this reason, we will not discuss this disease further in this chapter. eutrophication in water reservoirs or semi-enclosed water bodies leads to the formation of intensive phytoplankton blooms. during recent years, both the incidence and intensity of such blooms appear to be increasing, when examined at the global scale. this increasing severity of algal blooms may be a consequence of increasing levels of nutrient enrichment as a result of sewage disposal, increased agricultural runoff, and changes in hydrological regimes potentially related to climate change (unep, 2002) . blooms caused by toxic cyanobacteria (harmful algal blooms) lead to outbreaks of disease and dete riorated recreational and aesthetic values, causing both economic losses and illness and death of both humans and animals. in evolutionary terms, cyanobacteria are one of the oldest organisms on earth, dating back to more than 3000 ma (schopf, 2000) . they are oxygenic photosynthetic prokaryotes possessing the ability to synthesize chlorophyll a as their photosynthetic pigment. the nitrogen-to-phosphorus ratio (n:p) has been frequently used as a key indicator in predicting algal biomass and compositions, and its seasonal succession in lentic systems (tilman, 1982; kilham, 1990) . smith (1983) pointed out that bloom-forming cyanobacteria had a tendency to dominate in a lake when the n:p ratio was less than 29. the significance of the n:p ratio as a critical factor, however, is still controversial, due to the variability of the other chemical char acteristics and phytoplankton composition within a geographic region. for example, cyanobacteria blooms can be induced by increases in the phosphorus concentration instead of by a decrease in the n:p ratio (trimbee and prepas, 1987; sheffer et al., 1997) . cyanobacteria ( figure 8 ) produce a variety of toxic com pounds known as cyanotoxins. the impacts of cyanotoxins on human health have been of increasing concern, as the impacts of cyanobacterial blooms on water supplies as well as nearshore marine ecosystems have become better understood. outbreaks of poisoning from cyanobacterial blooms can be catastrophic, such as the death of 50 dialysis patients following exposure to inadequately treated water from the tabocas reservoir in brazil (pouria et al., 1998) or the hospitalization of 140 children and 10 adults who drank cyanobacterially contaminated water impounded by the solomon dam in australia (hawkins et al., 1985) . cyanobacterial toxins have also been implicated in mortality in wild fisheries and terres trial mammals, and can accumulate in the ecosystem . toxins are classified by how they affect the human body (who, 2001c): hepatotoxins (which affect the liver) are produced by some strains of the cyanobacteria microcystis, anabaena, oscillatoria, nodularia, nostoc, cylindrospermopsis, and umezakia. neurotoxins (which affect the nervous system) are produced by some strains of aphanizomenon and oscilatoria. cyanobacteria from the species cylindroapermopsis raciborski may also produce toxic alkaloids, causing gastrointestinal symptoms or kidney disease in humans. not all cyanobacteria of these species form toxins and it is likely that there are other as-yet unrecognized toxins. further, cyanobacteria produce a wide range of secondary metabolites, among which new cya notoxins continue to be found. besides the recognized effects of the toxins mentioned above, a recent study opened up a discussion about possible new causes of known neurodegenerative illnesses. cyanobacterial strains were found to produce the neurotoxic nonprotein amino acid, β-n-methylamino-l-alanine (bmaa) (cox et al., 2003 (cox et al., , 2005 . the bmaa is considered a possible causative agent of human motor neuron disease, amyotrophic lateral sclerosis parkinsonism/dementia complex (als/pdc), and has been found to accumulate in brain tissues of patients with progressive neurodegenerative illness (murch et al., 2004) . this was first detected in humans as a consequence of dietary habits and biomagnification in terrestrial ecosystems in guam (cox et al., 2003) . however, sometime later, bmaa was detected in aquatic ecosystems, such as in seawater in the area of a trichodesmium bloom and in freshwater and brackish waterbodies (metcalf et al., 2008) . cox et al. (2005) isolated bmaa in several species of free-living cyanobacteria. possible implications of these findings (cox et al., 2005; ince and codd, 2005) are that bmaa of cyanobacterial origin might occur in diverse natural and controlled environments where massive cyanobacterial populations occur. because these environments can include waterbodies used for drinking and recreational use, bmaa in drinking water may contribute to chronic intoxication. this may involve incorporation of the neurotoxin into an endogenous protein reservoir with slow release (murch et al., 2004) and a possible lag between expo sure and effect of years or decades. since protein-associated bmaa can accumulate within food chains, it is possible that biomagnification of bmaa occurs in marine ecosystems in a way similar to that in terrestrial ecosystems (banack et al., 2007) . thus, production of bmaa by marine cyanobacteria may represent another route of human exposure to this neuro toxin. cox stated that the bmaa produced by the algae may act as a slow toxin. for these reasons, it would be advisable to monitor bmaa concentrations in drinking waters contami nated by cyanobacterial blooms and in fish and animals that may be ingesting the microbes, even at low environmental densities. this can be particularly relevant in semiarid or arid regions that are highly dependent for their drinking water supply on reservoirs, in which cyanobacteria can regularly occur on a seasonal basis, normally in summer. fertilizer use, widespread cultivation of leguminous crops, and fossil fuel burning have produced strong changes in the global n cycle (galloway et al., 2004) . more than half of all n fertili zers ever used in earth's history has been applied in the past two decades (howarth et al., 2002) . moreover, increased n loading in the environment often occurs together with that of phosphorus. in freshwater ecosystems in particular, a com bined increase in both n and p is highly likely to drive eutrophication and associated significant ecological change. mckenzie and townsend (2007) reviewed direct and indirect evidence that changing global nutrient cycles are influencing the dynamics and incidence of pids ( figure 9 ). some of the disease agents discussed earlier in this chapter could react particularly sensitively to increased n and p loads. although generalizations are difficult, the evidence presented by these authors, together with past reviews by lafferty (1997) and townsend et al. (2003) , suggests a trend in which most asso ciations between increased nutrients and disease are positive. a parasite or pathogen may respond to nutrients directly, that is, without requiring an intermediate or vector host; or an inter mediate or vector host may respond to nutrients, mediating the overall disease response. there can be an increase in vector host population density as a result of increased primary productivity, or a decrease in population due to some disturbance related to nutrient addition, in both cases resulting in changes in transmis sion success of the parasite or pathogen (anderson and may, 1978; dobson, 1990; arneberg et al., 1998) . besides the above-mentioned increase in cyanobacterial blooms, increased nutrients could particularly affect ecological processes associated with, for example, malaria, schistomiasis, cholera, and filariasis, leading to a higher occurrence of these diseases. for example, vector-borne pathogens that cause malaria and schistosomiasis involve intermediate hosts (mos quitoes and snails) whose growth and reproduction depend on algae or weed abundance in their respective environments. where n additions cause greater plant growth and/or changes in plant species composition, the density of these intermediate hosts is also likely to be affected, with cascading consequences for the risk of disease. lafferty (1997) reviewed parasitic responses to a suite of environmental changes and found that, in most cases, eutrophi cation caused an increase in parasite abundance. johnson and carpenter (2008) suggested that planorbid snails in nutrient-rich environments grow faster. larger individuals are able to produce significantly more trematode cercariae at a faster rate. the avail able evidence suggests that, in general, nutrient additions should favor trematode development and increase disease risks. in the case of cholera, the bacteria display a strong associa tion with marine plankton, and, therefore, factors that cause increases in plankton primary productivity can also increase the prevalence of v. cholerae. thus, nitrogen-based eutrophication of coastal regions (nrc, 2000) has been linked to increased cholera risks (epstein, 1993; colwell and huq, 2001) , prob ably as an indirect response to plankton dynamics. changes in the n cycle are not globally uniform (galloway et al., 2004) . the largest changes have occurred in industria lized countries but the focus of global change is shifting to tropical and subtropical countries, where greatest relative changes in the n cycle over the next 50 years are expected (galloway et al., 2004; dentener, 2006) . for example, the booming soybean agriculture in brazil in the last decade is leading to rapid increases in regional n deposition and nutrient loading to aquatic ecosystems (martinelli et al., 2006) . similar increases are occurring throughout tropical and subtropical portions of asia and central america. these same regions harbor the greatest diversity of human pids (guernier et al., 2004) , including those that currently cause the majority of pidrelated human deaths (who, 2004b) . thus, the next decades will probably bring an increase in the potential for nutrients, especially n, to affect parasitic and infectious diseases in these regions. the changes in temperature and rainfall regime in temperate regions and the changes in land use resultant from them or from market shifts can exacerbate that potential. diseases produced by viral infections can emerge, reemerge, and be transmitted by several different, but often interlinked, mechanisms involving tight interactions between man and domestic and wild animals sharing artificial or natural aquatic systems. table 5 summarizes some viral diseases of worldwide relevance. in the following section, we will focus on avian influenza due its multiple and complex connections with the dynamics and use of wetlands by man and animals. 10.12.2.5.1 influenza: human and animal links between artificial and natural wetlands nutrient reduction in wastewaters or surface waters is a prior ity for reducing risks to human health. nevertheless, from the point of aqua-and agriculture, the nutrients contained in wastewater are a valuable resource, in particular in arid and semiarid regions. wastewater form has been used for aquaculture, for example, in duck ponds, in several countries, mainly in asia, for centuries to produce human food. organizations such as who, food and agriculture organization (fao), etc., have developed guidelines for the safe use of wastewater, excreta, and gray water in agriculture and aquaculture in order to provide a basis for the develop ment and implementation of health risk assessment and management approaches, including standards and regula tions, to address hazards associated with human waste-fed aquaculture (edwards, 2008) . however, wastes and fecally polluted surface water are often used without any pretreat ment or assessment of the presence of pathogens. various hazards are associated with waste-fed aquaculture: excretarelated pathogens (bacteria, helminths, protozoans, and viruses), skin irritants, vectors that transmit pathogens, and toxic chemicals. wastewater systems were also developed independently in india from the 1930s, in china from the 1950s, and in vietnam from the 1960s onward, but they were designed primarily for aquaculture, not to treat wastewater. few engineered waste water-fed aquaculture systems have been developed recently. systems primarily engineered to treat wastewater that incorpo rated aquaculture were developed in germany from the end of the nineteenth century, but only the munich system remains, and only for tertiary wastewater treatment and currently as a bird sanctuary (edwards, 2008) . in this, the following aspects in the dynamics of bird popu lations are of ecohydrological and biomedical relevance. during migratory movements, birds carry pathogens that can be transmitted between species at breeding, wintering, and stopover places where numerous birds of various species are concentrated, such as wetlands. a study by jourdain et al. (2007) focused on bird migration routes to the camargue in relation to risk of pathogen dispersion into western mediterranean wetlands. they considered two pathogens clo sely associated with wild birds: avian influenza (ai) virus and west nile virus (wnv). the ai viruses have a water-borne transmission, and ducks are their main natural reservoirs (easterday et al., 1997; alexander, 2000) ; wnv has a vectorborne transmission, and passerines are believed to play a major role in the amplification cycle (hurlbut, 1956; malkinson and banet, 2002) . despite different transmission cycles and ecology, both viruses are known to be carried by reservoir birds during migration and have been associated with emer ging disease transmission risk for humans and domestic animals (rappole et al., 2000; reed et al., 2003; olsen et al., 2006) . environmental conditions, avifauna abundance, and diversity, as well as the interactions among birds from different species and departure sites in stopover wetlands, may be of key importance in terms of virus communication (hudson et al., 2002) . for water-transmitted pathogens such as ai viruses, the risk of transmission may be associated with the number of ducks congregated on the same water body, particularly in autumn and winter. this crowding of wintering species, in addition to the permanent presence of a transient population of birds using wetlands to stop off during migration, could provide the conditions for the circulation and rapid dissemi nation of ai viruses. for vector-transmitted pathogens such as wnv, transmission possibilities depend both on reservoir bird density and on the dispersion capability and activity periods of the arthropod vectors. the risk for interspecific transmission of disease is particularly problematic when wild and domestic species are involved. ducks are the aquatic birds most likely to come in contact with free-range poultry, especially because the presence of congeners can induce migrating wild ducks to make a stopover (jourdain et al., 2007) . the study by jourdain et al. (2007) showed that western mediterranean wetlands are a hub for birds from several differ ent origins in central asia, siberia, northern and eastern europe, western africa, and the mediterranean basin. as exam ple for the potential of wetlands for introduction or reemersion of these viruses, they state that wnv dispersion by birds migrat ing from sub-saharan africa might explain why an outbreak occurred in 2000 in the camargue, even though the virus had not been observed there since the 1960s. besides migration, breeding ducks in the aquaculture ponds can increase virus circulation between ducks, water, sediment, fish, and man. in a study (markwell and shortridge, 1982) of the occurrence and persistence of influ enza viruses (hong kong type) within domestic duck communities, the virus was isolated throughout the year from feces or pond water or both, indicating a cycle of water-borne transmission. infection was asymptomatic and virus persistence in the duck community appeared to be dependent upon the continual introduction of ducklings sus ceptible to infection onto virus-contaminated water, since the feces of ducks 70-80 days old were generally virus-free despite the ducks' exposure to the virus in pond water. the normal practice of raising ducks of different ages on the same farm, where the water supplies are shared (figure 10) , appears to be instrumental in maintaining a large reservoir of influenza viruses in the duck communities. domestic ducks may act as a silent reservoir for the h5n1 ai virus. the concern is greatest in rural areas of affected countries, where traditional free-range ducks, chickens, and wildlife frequently share the same water source. domestic ducks can harbor the virus for long periods and without showing any sign of illness. an altered role for domestic ducks is further supported by evidence that the h5n1 virus circulating in parts of asia has increased its virulence in chick ens and mice (a laboratory model for mammals), and has expanded its host range to include larger mammals (e.g., cats and tigers), not previously considered susceptible to infection (fao, 2004) . the assessment of respective roles of routes and timing of wild waterbird migration and poultry imports is of utmost importance in order to objectively identify the origin and pos sible evolution of an outbreak in a determined country. for example, the avian flu outbreak in nigeria in 2006 may have been caused by the supply of infected live poultry including day-old chicks from different sources, including east asia and turkey, and not by wild waterbirds. this is supported by sam plings of 5000 wild waterbirds in african wetlands, in which no evidence of the h5n1 virus was found, indicting that wild birds probably played a relatively minor role in the spread of ai in that region. northward migration of wild birds from africa to europe in the northern spring of 2006 did not cause any major outbreaks. nor do wild birds seem to play a role in indonesia, where h5n1 has been present for some years and several cases of human infections have been recorded. however, although not many major outbreaks took place in europe in 2006, there is evidence to suggest that wild birds did play a significant role in spreading the disease on the european continent (aiweb, 2006). useand scarcityon human health: some examples from aquaculture, megacities, dams, and intensive agriculture aquaculture in or close to wetlands is increasing worldwide. besides being responsible for massive wetland destruction, aqua culture itself faces serious problems, arising from several diseases that can affect shrimp ponds. among the groups of microorgan isms that cause serious losses in shrimp culture, the best known are bacteria because of the devastating economic effects they have on the affected farms. as mentioned before, vibrio organ isms attach themselves preferentially to chitin surfaces, such as in zooplankton and shrimp exoskeletons. bacterial diseases, mainly due to vibrio, have been frequently reported in penaeid shrimp culture systems. at least 14 vibrio species are implicated in disease outbreaks in shrimp, including vibrio harveyi, v. alginolyticus, v. vulnificus, v. parahaemolyticus, and v. cholerae (non-o1) (venkateswara, 2008 ; figure 11 ). vibrios can produce different chitinases to degrade various chitin types (svitil et al., 1997) in marine, estuarine, and figure 11 example of vibrio disease affecting shrimp. in such severe cases, extensively melanized black blisters can be seen on the carapace/ abdomen of the infected animals. copyright national institute of oceanography, dona paula, goa, india, 1998. pond and irrigation canal next to live poultry markets. in http://www.eastwestcenter.org/index.php?id=5518&print=1 freshwater environments. further, meibom et al. (2005) found that v. cholerae can acquire new genetic material by natural transformation during growth on chitin. thus, natural compe tence occurring in chitin-attached bacterial communities can act as a powerful driver of v. cholerae evolution, which could be accelerated by environmental events such as high nutrient input, giving rise to copepod blooms. it is still unclear whether growth on a determined type of chitin substrateand the production of the corresponding specific chitinasespromotes the capture of external genetic material by vibrios. this empha sizes the need for biogeochemical characterization of different aquatic microhabitats, such as different types of chitin-contain ing particulate matter, besides living zooplankton, in environmental studies of vibrio diversity and virulence. as organic-matter-rich aquatic environments contain multiple microbial strains and species and high concentrations of bac teriophage and free dna, horizontal gene transfer (hgt) provides the most likely explanation for why vibrionaceae have developed high levels of genomic diversity (meibom et al., 2005) . interestingly, the cholera toxin gene (ctx) is a phage-mediated mobile genetic element that is transferrable to genetically closely related bacterial strains. in the aquatic environment, vibriophages can regulate seasonal disease out breaks, for example, seasonal cholera epidemics in dhaka were inversely correlated with the prevalence of environmental cho lera phages (faruque et al., 2005) . the v. cholerae (non-o1) is frequently isolated from sewage, estuarine waters, and seafood in cholera-endemic and noncholera-endemic countries. it has been associated with sporadic episodes of diarrhea worldwide, but has not caused pandemics. interestingly, in 1990, there was the first report of an epidemic of diarrhea caused by v. cholerae non-o1 that produces heatstable toxin, affecting khmers in a camp in thailand. in con trast to the v. cholerae o1 isolated from the same camp, in 93% of the cases, the non-o1 were resistant to three or more anti biotics (bagchi et al., 1993) . this calls attention to several important aspects in relation to threats to human health. the fact that the toxin is heat stable could imply a higher diarrhea risk for humans consuming cultured seafood as cooking would not completely eliminate toxin activity. its higher resistance to antibiotics compared with v. cholerae o1 potentially increases the disease hazards associated with these non-o1 strains. further, as mentioned previously, the abundance of chitinac eous substrate can favor mutations. thus, just as v. cholerae o1 evolved from a nonpathogenic to a pandemic-causing form (faruque et al., 2003) , it cannot be excluded that the high individual density of aquaculturein the same way as megacitiescould be favoring the emergence of new and highly pathogenic vibrio types. in many of the world's cities, water management and sanitation are in crisis and will dramatically worsen with the continuing growth of cities and slums. sewage pollution is the largest and most common type of pollution and one of the most common causes of illnesses. illnesses caused by sewage pollution are estimated to affect the health of more than 120 million people at any one time. contaminated water, inadequate sanitation, and poor hygiene cause over 80% of all disease in developing countries; diarrhea is the world's second most serious killer of children, but paradoxically in 90% of cases it could be easily prevented or treated. pollution of water sources by sewage contributes to 4 billion cases of diarrhea in the world each year, killing some 2.2 million children under the age of 5. poor sanitation currently affects 2.5 billion people, 40% of the world's population, who lack access to even the most minimal toilet facilities. the number of people without sanita tion will double to almost 5 billion in 2025, as the world becomes more urbanized (anonymous, 2002) . some 160 000 people are moving to cities from the country side every day. at least 600 million people in africa, asia, and latin america now live in squatter settlements without any sanitation whatsoever. the pollution of rivers and groundwater by sewage spreads disease and causes environmental degrada tion. in latin america, as a whole, only 2% of sewage receives any treatment. in asia, the level of sewage in rivers is 50 times higher than the united nations (un) guidelines. levels of suspended solids in asia's rivers almost quadrupled since the late 1970s. every minute 1.1 million liters of raw sewage are dumped into the ganges river (vidal, 2002) . most megacities are in asia. dhaka's population rose from 250 000 in the early 1970s to ∼12 million today, including the metropolitan area, and will probably reach 23 million in 2015. in the same time, kolkata's population grew from 3 to 5 million; including the metropolitan region, its population is 13 million and is predicted to reach 17 million in 2015. pakistan experienced one of the highest growth rates of popu lation worldwide: it quadrupled in only 60 years to over 170 million in 2008 (prb, 2008) . according to the world bank, karachi is one of the fastest-growing megacities of the world and is expected to rank seventh by the year 2015 (kamal, 2005) . the country faces a serious situation in terms of water availability, depletion, and pollution of its water bodies and irrigation systems as well as a severe degradation of its coastal ecosystems. this complex and multifaceted setting will be clo sely analyzed in the following sections. it has been reported that at least 12 of the 18 towns of the city are supplied with water unfit for human consumption, in most cases infected with escherichia coli. only around 30% of the total sewerage generated by karachi at present is treated. the e. coli, found in human feces, and other bacteria found in drinking water could cause life-threatening diseases, including diarrhea and cholera. the bulk of the drinking water concerned is taken from the indus river. bacteria easily enter the drinking water as the pipelines are rusted and leaking (irin, 2004) . lowintensity seismic activity, though normally not felt by people, probably further damages worn-out pipelines. additionally, due to the water shortages, the pipelines remain empty for a considerable amount of time daily, during which time they develop negative pressure and absorb moisture and sewage that has leaked from the nearby, similarly worn-out sewers. additionally, after rains, rainwater mixes with sewage and gar bage can enter the pipelines through the leaks to contaminate the drinking water supply, making people vulnerable to numer ous health hazards (hasan, 2008) . karachi is situated in a desert. however, in a study by sheikh et al. (1997) the analysis of microbiological data for the period 1990-96 showed the permanent presence of cholerawith seasonal periodicityin karachi. cholera cases peak each year between may and august in both epidemic and nonepidemic years. both v. cholera o1 and o139 serogroups were involved in the outbreaks in 1993 and 1994; o139 disappeared in 1996. the role of rain in disease seasonality and incidence is not clear. rainfall is scarce and sporadic, usually only between june and august. in 1994, the city could have been flooded, with wide spread overflowing sewers, whereas, in 1993, there was virtually no rain at all. cholera appears each year before the rains, and epidemic years in the 1990-96 data set appear to have occurred independently of rainfall. like most enteric diseases in an endemic setting, cholera in karachi is a disease of young children. the mean age of patients with acute cholera in karachi closely resembles that in the rest of the indian subcontinent where social conditions are com parable. despite this association with poverty, 9% of the patients in the study were admitted to expensive private rooms in good hospitals. this shows that, in a city with a sanitary infrastructure like that of karachi, personal wealth affords no protection (sheikh et al.. 1997) . visitors and tourists are also at risk. in the same context, despite the common perception that bottled water was safe and pure, microbiologi cal tests showed that about 35% of 3500 samples of water supplied in many bottled brands tested all over the city was unfit for human consumption (hasan, 2008) . according to the same above-mentioned study, in 1993, the new strain of v. cholerae, serogroup o139, established itself in karachi and during 1993 and karachi experienced over lapping, but distinct epidemics of both strains. the serogroup o139 never wholly replaced serogroup o1, and by 1996 it had disappeared. at that time, it was still unclear whether the dis appearance would be permanent, or whether o139 would reemerge in subsequent epidemic years. karachi is in a semi desert area, and the strain may not be able to maintain itself outside the human host (sheikh et al., 1997) . this strain has also shown diminished ability to maintain its epidemic potential in bangladesh, and it has been suggested that one reason for this may be that it is less able to persist long term in the aquatic environment (faruque et al., 1996) . however, years later, in july 2002 and june 2003, cholera outbreaks were detected by a diarrhea surveillance system in a fisher village near karachi (siddiqui et al., 2006) . the first outbreak was caused by v. cholerae o139 and the second one by serotype o1. it would be erroneous to conclude that, because of the relatively small number of persons affected, these cases are not relevant in terms of public health. on the contrary, they should be considered extremely valuable indicators of environmental change, especially of aquatic systems, which provide an early warning of possible future trends for policymakers and sanitar ians. water source was a risk factor only in the first outbreak: a reservoir in the village containing brackish water was only used for washing utensils and clothes and for bathing. only illness caused by v. cholerae o139 was associated with the use of reservoir water, while o1 cases were not. washing the clothes of infected persons may have introduced the pathogen into the reservoir. this implies that v. cholerae o139 was probably able to survive for a time outside the body and in water long enough to infect other people. this may be partly because the water was salty and that v. cholerae is a salt-loving bacterium. in summary, fecal pollution, increased nutrients, turbidity, and sodium content create favorable conditions for the propagation of v. cholerae in pakistan's coastal zone, megacities, and irrigation systems. when the increasing pollu tantchemical and microbiologicalload reaches the coastal region, it encounters a disturbed wetland ecosystem (discussed in section 10.12.3.3.2), where vibrios could potentially multi ply and mutate to new pathogenic types. a close regular surveillance of vibrios at basin level, including in the coastal region, rivers, and channels, and in humans is essential in this region, which has the potential to become an epidemic center. further, restoration of riparian forests and wetlands habitat should be a priority to avoid further habitat loss, and potential host shifts, although salinization would probably preclude the reinstallation of the same species existent before dam building and population explosion. the hoogly river is the most important source for the water supply of kolkata. through an agreement with bangladesh, only a determined amount of water from the ganges can be diverted into the hooghly river during the dry season. although this does not increase the amount of pollution in the river, it does increase its concentration. during the mon soon, rubbish and feces are washed out from the city into the ground and into the river (karthe, 2002) . around 30% of the water supply is lost through leakages in the obsolete distribu tion network, reservoirs, and public water tap connections. however, the disposal of sewage is an even greater threat to human health. reduced capacity of the inadequate sewer net work, aggravated by obstruction caused by mud or garbage, as well as flooding during the monsoon produces pollution of surface and groundwater with enteric bacteria. as in karachi, interruptions or shortages in the water supply produce a negative pressure in the pipelines, which then absorb polluted water that had leaked from sewers and the surface, especially during the monsoon season. before and after the monsoon, water quality increases, that is, bacterial load decreases. following several cholera epidemics, the chlor ination of unfiltered water supply began in 1963. this reduced cholera incidence, but supply of potable water to many parts of the city is still insufficient. people in shanties frequently get untreated water from hydrants, or from the river (hensgens, 2005) . cholera seasonality in kolkata is further discussed in section 10.12.3.3.1. the situation in london 150 years ago resembled current conditions in many megacities in developing countries. by 1851, half of the population of britain was living in townsthe first society in human history to do so. over the previous 70 years, britain's population had risen at an unpre cedented rate. large towns were desperately unhealthy, with death from sickness at a level not seen since the black death (daunton, 2004) . london had a large scavenger class living off the refuse of the citya group so numerous that it could have formed the fifth largest city in england. new epidemics affected the citiescholera and typhoid were carried by polluted water, typhus was spread by lice, and 'summer diarrhea' was caused by swarms of flies feeding on horse manure and human waste. london suffered from recurring epidemics of cholera and in 1853-54 more than 10 000 londoners were killed by the disease (johnson, 2006) . the frequent occurrence of cholera in london gave impetus to legislation, enabling the metropolitan board to begin work on sewers and street improvements. by 1866 most of london was connected to a sewer network brilliantly devised by joseph bazalgette (bbc, 2009) . the flow of foul water from old sewers and underground rivers was intercepted and diverted along new, low-level sewers, built behind embankments on the river front and taken to new treatment works. by 1870, both the albert and the victoria embankments had been opened. the victoria embankment protected bazalgette's low-level sewer from the hydraulic pressure from the thames estuary. the chelsea embankment was completed in 1874. the public health act of 1875 required local authorities to implement building regulations, or bylaws, which insisted that each house should be self-contained, with its own sanitation and water. this change in the design of housing complemented the public investment in sewers and water supply. cholera never reappeared in london after that. london was the largest city on the planet in 1854, but now it is on the small side, in comparison to, for example, mexico city, são paulo, or mumbai. massive shantytowns have exploded at the margins of today's megacities. in such places, the water-borne diseasesincluding cholerathat plagued victorian london are still widespread, thanks to insufficient public health and sanitation resources. worldwide, up to a billion people live in shantytowns and according to some projections this will increase to a quarter of the world's popula tion by 2030 (johnson, 2006) . despite enormous progress in the molecular biology of v. cholera, still little is known about basic forces, such as spatial biogeochemical gradients, seasonal rainfall variations, or cyclones, driving its abundance, diversity, and virulence in the basins of rivers and estuaries of the indian subcontinent. the most recent detailed studies on seasonal variations of estuarine salinity and related urban cholera incidence are from the 1950s (chatterjee and gupta, 1959) . these compare the river systems kolkata-hoogly (a main branch of the ganges) and london-thames (data from the nineteenth century), and are discussed in miller et al. (1982) . an important aspect of the 1950s data is that minute but clearly delimited salinity oscillations (e.g., 0.01-0.15 and 0.05-1 ppt) in the hoogly river tightly correlate with cholera incidence in kolkata. several authors reported significantly higher salinity ranges for the growth and persistence of v. cholerae in the environ ment, for example, 2.5-30 ppt (miller et al., 1984) or 5-25 ppt (singleton et al., 1982; louis et al., 2003; randa et al., 2004) . salinities <1 ppt were considered suboptimal (miller et al., 1984) . however, kolkata's data clearly indicate cholera out breaks at much lower salinities. such oscillations could also be a proxy of other processes occurring at basin level, which were responsible for triggering the cholera outbreaks. vibrio survival at low salinities can be facilitated by adsorption onto algae, zooplankton, or by high nutrient concentrations. unfortunately, this information mostly originated from stag nant water bodies or short-term investigations (e.g., islam et al., 1994, 2007 and references therein) , but no studies are available about the seasonality of hydrology, biogeochemistry, and vibrio dynamics in flowing waters of the large rivers in this region through which vibrios most likely spread from the coastal zone toward inland habitats. since the 1950s, seven large dams for irrigation purposes have been constructed in india. the farakka barrage, complete in 1975, diverts the ganges river water into the hooghly river during the dry season to flush out the accumulating silt in the port of calcutta. it cuts off bangladesh's water supply, elevating salinity, and has affected fisheries, caused desertification, and hindered navigation, and poses a threat to water quality and public health (wolf, 2001) . there is evidence of changes in cholera seasonality due to hydrologic disturbances. before the 1970s, the peak cholera season in dhaka was november-february; now it is september-november. in kolkata, season ality has changed twice since the mid-1950s (niced, 1978 . these shifts may be related to changes in salinity, particle load, and associated estuarine biogeochemistry due to, for example, the construction of the farakka barrage on the river ganges (mirza, 1998) or increased melting of himalayan glaciers (unep, 2007) . more that 25 years ago, miller et al. (1982) postulated that dam construction in india could influence vibrio dynamics by salt intrusion. these aspects deserve further investigation; apart from the 1950s data, there are no other published data series systematically relating these parameters in the rivers of the region with cholera incidence. this informa tion is essential in order to evaluate the transboundary effects of dam construction and water management. dam construc tion in india has reduced riverine discharge in bangladesh, inducing desertification in its northern sector and facilitating salt intrusion into its estuaries, particularly in the southwestern region (wolf, 2001; adel, 2005) . this resulted in changes in land use from rice cultivation to shrimp farming in the southern bay of bengal (gebauer, 2007) (discussed in section 10.12.3.1). salinization of inland water bodies can facilitate the spreading of the halophilic vibrio organisms and affect drinking water availability. on the other hand, global warming increases glacier melting and associated riverine runoff. both factors, in a frame of increasing intensity and frequency of cyclones and flooding events, create an extremely complex situation in the coastal zone that could result in shifts in seasonal cholera patterns. despite the different overall climatic setting of pakistan as com pared to india and bangladesh, increasing water needs in pakistan are leading to a similar situation in the coastal zone, including increased cholera incidence. the common factors are the halophilic character of vibrio cholerae and other vibrios and the salinization of estuaries and inland waters. water needs for irrigation of desertic and semidesertic areas, as well as for drinking water supplies, mainly for karachi and islamabad, have led to the construction of several dams along the indus river. within the sindh province, there are three major barrages on the indus-guddu, sukkur, and kotri. severe reduction of water flow below the kotri barrage started affecting environments in the area from 1960s onward, with the following consequences in the river basin: (1) drying up and death of riparian forests, figure 12 the indus delta faces major degradation threats, whose major cause is the reduction in the flow of freshwater from the indus river. as the delta dries up and the mangrove forests decline, the sea is slowly sweeping in. which occurred soon after 1970; (2) reduction of the area under fruit and vegetable crops; (3) destruction of natural pastures causing a reduction in animal populations; and (4) desertifica tion leading to a shifting of human settlements. in the coastal region, intrusion of seawater in the river bed to a distance of 80 km upstream from the shore, with percolation of saline water from the riverine areas into groundwater of adjoining irrigated areas, has turned shallow water lenses brackish ( figure 12) . another reason for accelerated salinization in the indus river is the saline water discharges from the salinity control and reclamation program in the north-west frontier province, punjab, and india (hasan, 2008) . along the coast, the increase in salinity of seawater along the whole coastline of sindh has resulted in damage to man groves, colonization by other halophilic species, and the abandonment of ∼6500 ha of land reserved for shrimp farming by the government of sindh. sea shrimp can survive within salinity range of 17-27 of water, but in the space of 5 years , salinity rose beyond the tolerance limit. water salinity in sea creeks and estuaries increased from ∼25 to over 35 ppt, making estuaries inhabitable for some shrimp and other species of commercial interest. in conditions of low salinity, shrimp farming could have been established all along 320 km of seacoast. sea fish and prawn catch has declined considerably and severe erosion due to reduced sediment load occurs along the coast. in the coastal region, the livelihood of fishing communities and the fishing industry as a whole depends on ecosystem integrity. however, this has already been devastated by reclamation of former marine areas, and of mangrove marshes and mudflats. it desperately needs to be protected, for no city that destroys the ecology of the region where it is situated can be sustainable. the south asian tsunami gave ample proof of this and so did the flooding of karachi, much of which is the result of reclama tion from mangrove marshes, creeks, and natural drainage channels for elite real estate (hasan, 2008) . in addition to the deeply disturbed aquatic ecosystems described above, only 2% of cities with a population of over 10 000 have wastewater-treatment facilities. of the wastewater generated daily, 36% is used in agriculture and 64% is disposed of into rivers or the arabian sea (iwmi, 2003) . directly or indirectly, 90% of the people of sindh, in rural or urban regions, drink water from the indus. salt content at kotri reaches 0.60 ppt in winter months, and supplies to karachi range from 0.25 to 0.60 ppt (panhwar, 2000) . the combina tion of a riverine environment with increasing salinity, growing populations, lack of sanitation, input of untreated sewage, drinking water contaminated with enteric bacteria, and rela tively high sodium content is very similar to that in london during the cholera epidemics in the nineteenth century (see section 10.12.3.2.4). recently, a cholera outbreak in mirpur khas, a district of sindh province, has been reported (anonymous, 2008) . scientists at the university of health sciences found out that around 50% of the patients were affected by cholera instead, as was previously thought, by gastroenteritis. the authorities have been requested to pay particular attention to this outbreak of cholera, which could spread to the other areas of the province. mirpur khas has a population of ∼357 000, has successful agriculture, and is con nected to the indus via irrigation canals. the irrigation system of pakistan has been considered "one of the largest contagious systems of the world" by gachal et al. (2007) . the reservoir formed by the three gorges dam (tgd) is the largest in the world at over 600 km in length. studies about the impact of parasite dynamics have been restricted to medically important species such as schistosoma japonica (zheng et al., 2002) . these studies have focused on the distribution of the intermediate host oncomelania hupensis within the tgd area and associated downstream water bodies. before construction of the dam, neither o. hupensis nor s. japonica occurred in the reservoir region. however, it is widely predicted that the dam will lead to the introduction of s. japonica into the tgd region, while downstream both positive and negative effects on schistosomiasis transmission will occur (zheng et al., 2002) . nevertheless, a survey of the recently filled reservoir (jobin, 2005) concluded that because of the very steep shoreline along most of its length and subsequent narrow photic zone, which provides only a limited area for the growth of plants, there was little chance of o. hupensis, principally a marshland snail, becoming established. however, these unfavorable topo graphic conditions do not preclude other mollusk species colonizing the shoreline (morley, 2007) . for example, former gravel quarries converted into lakes have a steep-sided profile with a narrow discontinuous zone of plant life but support a diverse molluskan-trematode community (adam and lewis, 1993; morley et al., 2004) . river blindness is an important parasitic disease around tropi cal dams in africa, along the red sea in arabia, in central america, and in parts of south america. the rapids of the upper nile river used to be a classic focus of this blinding parasite, spread by the bite of a species of blackfly, which breeds in white-water habitats and on dam spillways. in uganda (jobin, 1999) , the history of river blindness can be traced to the owen falls dam in the upper nile river. this dam flooded out owen falls and also ripon falls near the outlet of lake victoria. the history of the impact from the owen falls dam on onchocerciasis over the last 50 years shows the importance of optimal water current velocity regulation for the avoidance of reduction of this and other water-borne dis eases such as schistosomiasis. prior to construction of the owen falls dam (figure 13 ), river blindness was endemic among the buganda people, downstream along the nile. in 1950, the prevalence of the parasite was 65%. to protect the workers, weekly applications of ddt were made at the outlet of lake victoria, treating the entire flow during the construction phase, and eliminating the blackflies for at least 50 km downstream. after dam completion in 1954 and discontinuation of ddt applications, the black flies did not return to their former habitats downstream of the dam. by 1974, the prevalence of the parasite had decreased to 0.2% among the populations along the river. the fact that blackfly populations did not return to former levels indicates that there must have been a change in the basic habitat condi tions in the river. the dam had two major hydraulic effects on the river: one effect of turbine operation is a reduction of velocities downstream. the preferred range of water velocity for breeding of the east african species of blackfly involved in river blindness is between 0.5 and 3 m s −1 . at present, the mean velocities downstream of owen falls dam are between 0.4 and 0.5 m s −1 , slightly less than the required velocities. prior to dam construction, the mean velocity was roughly twice the present, and thus highly suitable for blackfly breeding. yet, the major ecohydrologic effect of the dam reservoir was the complete submergence of owen falls and ripon falls upstream of the dam. these falls were preferential sites for blackfly breeding, and their permanent submergence eliminated the breeding completely. in west africa, dam construction has led to a significant switch in dominant water-borne diseases. the volta river basin extends over six west african countries (43% in burkina faso, 42% in ghana, and 15% in togo, benin, cote d'ivoire, and mali) and covers an area of about 400 000 km 2 . the volta lake is the largest man-made lake in the world, created after the construction of the akosombo dam in 1965. the primary purpose of the project was to supply cheap electricity to smelt aluminum, other significant uses being transportation, fishery, water supply (commercial and domestic purposes), tourism, and irrigation. construction of the volta lake led to the resettlement of about 80 000 people from several hundreds of villages. in the other riparian countries of the basin, small and larges dams have been built by governments, nongovernmental organizations (ngos), and local people to secure food produc tion after the severe droughts that occurred in the 1970s and 1980s. in the nakambe sub-basin (burkina faso) alone, more that 600 small dams have been built, mostly during that period (barry et al., 2005) . there have been serious health issues associated with the volta lake, in particular with two major diseases: schistosomia sis and river blindness. before the creation of the volta lake, schistosomiasis was endemic in ghana; but endemicity was low along the volta river. according to an epidemiological survey done in 1960-61 before the lake was formed, infection rates of schistosomiasis in the area had been 1-5%, mostly affecting children. in the asukwakwaw area, north of the akosombo dam, the prevalence of onchocerciasis is now almost 90%. principal public health impacts of the formation of the lake have included reduced prevalence of river blindness, but increased incidence of urinary schistosomiasis and a mas sive increase in malaria, as discussed in the following paragraphs. the dam virtually halted the rate of flow in the volta river, increasing stagnant water conditions and consequently creating ideal breeding grounds for carriers of water-borne diseases. in the period following the construction of the dam at akosombo, there has been a steady decline in agricultural productivity along the lake and the associated tributaries (gyau-boakye, 2001). the land surrounding lake volta is not nearly as fertile as the for merly cultivated land residing underneath the lake, and intensive agricultural activity has quickly exhausted the already inade quate soils. without the periodic floodings that brought nutrients to the soil, before the natural river flow was halted by the dam, upstream agricultural systems are also losing soil ferti lity (van de giesen et al., 2001) . the growth of commercially intensive agriculture has produced a rise in fertilizer runoff into the river. this, along with runoff from nearby cattle stocks and sewage pollution, has caused eutrophication of the river waters (gyau-boakye, 2001) . this nutrient enrichment, in combination with the low water movement, has allowed for the invasion of aquatic weeds (cerratophyllum) (fobil and attaquayefio, 2003) . these weeds, associated with the aquatic snail, the 'intermediate host', together with mass migration into the fishing commu nities from regions in which the disease was endemic, have led to a great increase in the prevalence of schistosomiasis in many localities around the lake. the presence of aquatic weeds along the lake and within tributaries has resulted in even greater devastation to local human health as they provide an excellent habitat not only for snails but also for mosquitoes (gyau-boakye, 2001) . before the construction of the akosombo and kpong dams, malaria was not much of a problem along the swift-flowing volta river, but, when it became a stagnant lake, it became a greater public health problem in lakeside villages. by 1979, urinary schisto somiasis had increased to become the most prevalent disease in the area, affecting some 75% of lakeside residents (gitlitz, 1993) and reaching a prevalence rate of 90% among children in certain localities. the problem of schistosomiasis in the lake basin must be seen as embracing both the lake and the volta delta. the migratory habits of the fishermen ensure the spread of the disease from endemic areas to other areas. in particular, resettlement villages have showed an increase in disease pre valence since the establishment of lake volta, and a village's likelihood of infection corresponds to its proximity to the lake. previously, the population in the basin generally lived away from the main watercourses because of the threat from water borne diseases. children and fishermen have been especially hard hit by this rise of disease prevalence (zakhary, 1997) . additionally, the degradation of aquatic habitat has resulted in the decline of shrimp and clam populations. the physical health of local communities has declined as a result of this loss of shellfish populations, as they provided an essential source of dietary protein (fobil and attaquayefio, 2003) . conversely, while leading to a dramatic increase in schisto somiasis, the lake has flooded out the riparian forests which constituted a breeding place for a species of tsetse fly, glossina spp. from the palpalis group, the vector of protozoan trypanosoma brucei gambiense, which causes the western african trypanosomiases (sleeping sickness) in people. the lake has also inundated and eliminated the major breeding sites of the onchocerciasis blackfly in rapidly flowing streams and rivers north of the akosombo dam. the construction of the second dam at kpong also eliminated the breeding sites downstream of akosombo and therefore stopped the transmis sion of river blindness in the vicinity. the main benefit to health because of the construction of the akosombo dam in 1965 and the kpong dam in 1981 is undoubtedly the reduc tion of the incidence of onchocerciasis in the volta basin. about 60 000 fishermen living mostly in isolated villages around the lake were exposed to the riverine disease and did not have access to health facilities (jobin, 2005) . increased global demand for biofuels has incentivized sugar cane plantation in brazil, giving rise to several social and environmental modifications (martinelli and filoso, 2008) . the widespread occurrence of generalist animal species in sugarcane areas has been associated with public health pro blems. for instance, the population increase of the semiaquatic rodent, capybara (hydrochoerus hydrochaeris), in the piracicaba river basin has led to the spread of brazilian spotted fever (bsf) (labruna et al., 2004) . the bsf is the most important tick-borne disease in brazil and is caused by the bacterium, rickettsia rickettsii, and transmitted by the tick, amblyomma cajennense, its main vector, and capybaras serve as host for the ticks (estrada et al., 2006) . r. rickettsii infections can cause a wide range of clinical manifestations, ranging from asympto matic or mild febrile illness to overwhelming and fatal disease. failure in diagnosis and delayed therapy have contributed to hidden mortality, frequently a result of atypical fulminant forms of the disease (gonçalves da costa et al., 2006 ) and physician's lack of knowledge about the disease, which is exa cerbated by the difficulty of adequate confirmatory laboratory tests during its acute phase. mortality can reach 40% of the infection cases. the bsf has been known in brazil since 1929. during the period between 1940 and the 1980s there was a marked drop in the number of reported cases of bsf in brazil, as well as in the united states (angerami et al., 2006) . however, since the 1980s an apparent reemergence of the disease has been observed with an increase in the number of reported cases in the southeast of brazil (angerami et al., 2006) . rickettsial diseases have been considered emerging zoo noses worldwide (raoult and roux, 1997) and should no longer be classified as rare diseases in brazil. despite the still moderate number of bsf cases, its increasing trend, together with high mortality rates, reflects and calls atten tion to deep changes in land use and habitat structure in brazil. increased fertilizer use, pollution, and soil erosion have caused deterioration of aquatic systems. as colluvium sediments are transported downhill across the landscape from sugarcane fields, they are deposited onto wetlands, and into small streams, rivers, and reservoirs. deposition affects water quality, and ecosystem biodiversity (politano and pissarra, 2005) and functions. high rates of n export into rivers draining watersheds heavily culti vated with sugarcane in brazil, such as the piracicaba and mogi river basins, have been reported (filoso et al., 2003) . the indus trial processing of sugarcane for production of sugar and ethanol is another source of pollution for aquatic systems with poten tially harmful effects for human health. waste products (vinasse) are rich in organic matter, and increase the biochemical oxygen demand (bod) of waters receiving these effluents, often causing anoxia (ballester et al., 1999) . with the boom of ethanol pro duction in brazil in the early 1980s, new legislation was enacted to ban the direct discharge of vinasse into surface waters. since then, nutrient and carbon-rich vinasse has been mixed with wastewater from washing sugarcane and is recycled back to sugarcane fields as organic fertilizer (gunkel et al., 2007) , although this practice is still far from generalized. as a conse quence, high nutrient concentrations in these effluents also contribute to the problem by enhancing algal blooms and pro moting eutrophication of surface waters (matsumura-tundisi and tundisi, 2005) . the increase and dispersion of the capybara population and the associated health risk is most likely due to a strong anthro pogenic habitat modification caused by extensive monoculture. paradoxically, this situation could be aggravated by current efforts to restore aquatic ecosystems. typical capybara habitat is com posed of two main components: water and a patch of forest or woodland. in são paulo state, capybaras and ticks share a habitat component, the riparian vegetation called gallery forest. these forests form as corridors along rivers or wetlands and project into landscapes that are otherwise only sparsely wooded, such as savannas, grasslands, or deserts. the boundary between gallery forest and the surrounding woodland or grassland is usually very abrupt, with the ecotone being only a few meters wide. in são paulo state, capybaras shelter in the gallery forest and feed in the sugarcane fields adjacent to the ecotone ( figure 14) . thus, the abundant food and lack of predators in this new habitat have led to a strong population increase (labruna, 2009 ). in the 1950s, the capybara was considered in danger of extinction in são paulo state, where population can reach densities 60 times higher than in natural environments in some areas, such as the extended wetlands of pantanal (verdade and ferraz, 2006) . this offers optimum conditions for the increase in the tick and rickettsia population. further, the capybara is a protected species and is gradually adapting to aquatic urban habitats with a larger spectrum of possible vertebrate hosts for ticks ( figure 15 ). capybaras have been observed in the outskirts of são paulo city along the highly polluted pinheiros river (labruna, 2009) , which flows through the fourth largest metropolitan area worldwide, with ∼11 million inhabitants. presently, a substantial cleanup pro gram for this river is underway and an increase of secondary vegetation and fragmented, regenerated systems is expected. with this, a further expansion of capybaras, ticks, and bsf toward anthropogenically modified habitats, including urban and suburban areas close to water sources such as rivers and lakes, is likely. in addition, it has recently been reported (meireles et al., 2007) that capybaras in the são paulo state were infected by cryptosporidium parvum, which is a protozoan pathogen that causes a diarrheal illness called cryptosporidiosis, an acute short-term infection that can become severe and chronic in children and immunocompromised individuals. despite not being identified until 1976 (meisel et al., 1976; nime et al., 1976) , it is one of the most common water-borne diseases and is found worldwide, being spread by direct ingestion of con taminated water or food and through recreational water activities. the finding of zoonotic c. parvum infection in this figure 14 aerial photo of a sugarcane plantation and a small water body with highly fragmented remains of riparian forest, brazil. photo credit: geraldo arruda, jr. semiaquatic mammal that inhabits anthroponotic habitats raises the concern that human water supplies in brazil may be contaminated with cryptosporidium oocysts from wildlife. cryptosporidiosis is the most significant water-borne dis ease associated with the public water supply in western europe. when contamination occurs, it has the potential to infect very large numbers of people. some notable outbreaks of cryptos poridiosis have been associated with heavy rainfall events. in this chapter and elsewhere (despommier et al., 2007 and references therein) , there are indications that the boundaries between ecological systems play a role in some of the most important emerging infectious diseases, with a correspondence between ecotonal processes and the ecological and evolution ary processes responsible for zoonotic and vector-borne infections. terrestrial ecotones include forest-edge habitats, fragmented forest landscapes, and forest-grassland interfaces. terrestrial-aquatic ecotones are found in riparian habitats, riverine landscapes, freshwater and estuarine wetlands, and in the coastal zone. anthropogenic ecotones can include crop land/pasture-natural habitat and settlement-natural habitat, and a combination of these. processes in ecotones can contribute to the shifts or changes in hosts, vectors, or pathogens that produce disease emergence. these dynamics are associated with changes in land cover/use and with the changing nature of the land-water interface. anthropogenic influences can intensify ecotonal processes by increasing their geographic extent and overlap. various ecotone features can contribute to disease emergence. animals congre gate in ecotones. populations of species that normally are members of distinct ecological communities from different habitats or ecosystems overlap in ecotones, facilitating patho gen spillover. host-vector hyperabundance increases the potential for pathogens to achieve critical threshold density. enhanced dispersal conditions facilitate dispersal at a higher rate or over longer distances, along linear habitats defined by habitat edges, such as riverine or gallery forest, and flowing water in streams or rivers themselves. cropland-forest-river transitions appear particularly relevant as sensitive indicators of change in this context. for example, the transition between fragmented riparian habitats such as degraded gallery forests and, for example, sugarcane fields seems to be a priority sector for the control of rickettsia-related diseases since capybaras must cross the ecotone to feed on sugarcane, as described else where in this article. further, nutrient pollution, degradation of riparian habitat, and the loss of ecological functions involving assimilation of nutrients and pathogens, combined with high concentrations of domestic fowl and their waste, are commonly associated with human settlement/aquatic-terrestrial ecotones. the emer gence of ai involved the mixing of three different communities: wild migratory waterfowl (wetlands), wild local birds, and domestic fowl (ponds), and, later, also pigs. like influenza, the emergence of japanese encephalitis has involved transmis sion in the spatial area of overlap of human settlements, agriculture, and natural habitat (despommier et al., 2007) . while waterbirds and wetland habitat are implicated in influ enza, nonaquatic wild birds and irrigation systems provide the vector habitat for encephalitis. the intensification and expan sion of irrigated rice production systems in southeast asia over the past 20 years have made an important contribution to the spread of this disease, which is produced by a mosquito-borne virus (see table 5 ). the flooding of the fields at the start of each cropping cycle leads to a sizable increase in the mosquito population. domestic pigs and wild birds are reservoirs of the virus and transmission to humans may cause severe symptoms. japanese encephalitis is a leading cause of viral encephalitis in asia with 30 000-50 000 clinical cases reported annually (who, 2001d) . in general, research in ecotoneparticularly terrestrialaquatic dynamicscan provide vital information about changes in climate, river hydrology, sea level (cohen and lara, 2003) , and land use (lara et al., 2002) . a strengthened integration of ecological and biomedical monitoring is essen tial for successfully restoring ecological functions and enhancing environmental and human health. globally, the surveillance of locally and regionally relevant ecotones could provide evidence of disease emergence related to environmen tal change. in this context, restoration of lost ecological functions, such as nutrient sequestration by wetland creation or regeneration of riparian vegetation, must be accompanied by careful monitoring of other changes in the surrounding land scape and in the connectivity between basin processes and land use. created or regenerated aquatic systemsindependently of their purposewill increment existing ecotonal processes or generate new ones. thus, surveillance of the created/recovered/ enhanced system ecological functions should include at least those disease agents (host, vectors, or pathogens) , which according to the present knowledge would have a higher prob ability of proliferation under modified or changing conditions (e.g., mosquito larvae in temperate wetlands and snails in tropical regions). floods and droughts will intensify with climate change and affect health through the spread of disease resulting from habi tat modification, with high risk of rapid increase in diarrheal and other diseases (lipp et al., 2002; ipcc, 2007) . there are many pathways through which hydrologically relevant events can affect health; notably when a river or stream bursts its banks producing changes in mosquito abundance (malaria, and dengue), or contamination of surface water with human or animal waste such as, for example, rodent urine (leptospiro sis). flooding may become more intense with climate change and can result in the spread of disease. conversely, droughts can produce changes in vector abundance if, for example, a vector breeds in ponds left in dried-up riverbeds (noji, 1997; menne et al., 1999) . coastal ecosystems and their basins are rapidly changing due to anthropogenic pressure and global warming, also inducing changes in patterns of resource use (lara et al., 2002) . integrative, comparative approaches are needed for the understanding of functional links between basin structure; morphology of different estuaries, marshes, and mangroves; flooding and biogeochemical regimes (lara and cohen, 2006) ; pathogen life cycles; and disease incidence (wolanski et al., 2004; lara et al., 2009) . for improved prediction of the dispersal of inundation waters, formation of drought ponds, or preventive identifica tion of vulnerable locations or sectors that could be used as drainage areas, it is crucial to have a detailed knowledge of the regional and local topography. the elaboration of highresolution topographic models (dem) of basins in connection with hydrology, meteorology, and biogeochemistry data will also allow the assessment of vulnerability descriptors such as soil moisture potential, salinity, or organic matter content, which can be crucial state parameters for the development of microorganisms and/or disease vectors. however, precisely in tropical coastal areas, where the impact of climate change on vector-transmitted diseases is of high concern, there is frequently a lack of topographic informa tion with an adequate resolution for low-lying sectors. in vulnerable regions, the combination of risks to both food and water can exacerbate the impact of even minor weather extremes (floods and droughts) on the households affected (webb and iskandarani, 1998) . a methodological approach including wetland basin microtopography and its relation with inundation dynamics and estuarine biogeochemistry is necessary for vulnerability assess ment and risk management. the use of geographic information systems (giss) provides an excellent basis for network coopera tion at the interfaces between environmental and biomedical research, adding a critical componenthuman healthto coastal management research. this is a major concern for the who, which also has set a priority on the link between gis and disease surveillance (who, 2000) . through the joint who/united nations children's fund (unicef) program health map, specific gis software was developed for that purpose, combining a standar dized geographic database, a data manager, and a mapping interface. however, although these concerns are closely linked to the subject matter of ecohydrology, they are not usually included in interdisciplinary research projects dealing with, for example, coastal wetlands. clearly, the only way to concretely reduce vulnerability is to ensure that infrastructure is in place for the removal of solid waste and wastewater and the supply of potable water. no sanitation technology is safe when covered by floodwaters, as fecal matter mixes with floodwaters and is spread wherever the floodwaters run (lara et al., 2009) . consideration should also be given to the deterioration of groundwater quality caused by salinity intrusion due to climate change and rising sea levels (e.g., sherif and singh, 1999) . thus, as stated in section 10.12.1.1, such health issues clearly require a basin approach, that is, considering basins as a natural unit of territorial management. however, a usual shortcoming of gis-derived vulnerability studies is that data sources from official institutions are most frequently based on municipalities or counties as an administrative unit, whose limits do not necessarily coincide with basin boundaries. thus, this vision of the relationship between climate and sealevel change and effect on human health converges with zalewski's (2002) statement that: as a consequence, the issue of water quality at the basin scale cannot be resolved without a profound understanding of the effects of hydrology on biotic processes and of biota on hydrology. the frame work for developing the principles of ecohydrology is logically the water basin scale. (zalewski, 2002: 825) creation of wetlands for nutrient sequestration from surface waters requires the inclusion of measures for control of locally major and regionally relevant disease vectors such as snails or mosquitoes. the latter are relevant for disease transmission in several climatic zones besides the tropics, and global warming is widening their habitats with severe consequences for human health (e.g., the dengue outbreak in argentina in 2009) and will therefore be treated with some detail. early methods of managing salt-marsh mosquitoes have primarily focused on maximizing the reduction of mosquito populations, with mini mizing environmental impact as a secondary consideration. however, in the last few decades, there have been attempts to apply diverse water management models to marsh systems, especially in terms of vector control and habitat modification (dale and hulsman, 1990; wolfe, 1996) using programs with minimal environmental impacts. the success of these programs requires a thorough knowledge of mosquito developmental conditions, as well as potential impacts on adjoining ecosys tems. a deep knowledge of the local microtopography and tidal regimes is critical. marsh drainage and hydrological linkage to the tidal source are essential in the determination of what type of wetland occurs where, and for the development of appro priate wetland management measures. elevation of a few centimeters is more critical in the coastal wetlands than that of hundreds of meters in the mountains. in this section we cover not only well-established methods for mosquito control, but a series of successful methods for snail control derived from good agriculture practice, basically from techniques for rice cultivation. ecohydrology can contri bute to and learn from these experiences. water management, molluskicides, and chemotherapy have been the main instruments for preventing or treating schisto somiasis. biological control of snails through predators such as ducks, fish, turtles, crustaceans, water rats, leeches, and aquatic insects have been also used, as yet with very limited success. an interesting lesson on the potential for improved water management to reduce vector proliferation from the 1960s can be drawn from the experience in the baluchi irrigation scheme in then tanganyika (sturrock, 1965) . this system was remark ably clear of snails, although several species occurred in small numbers. several factors may account for this. first, the water flow in the canal system was very rapid when it was in use, but the canals were completely dried out in the dry season. second, silt and vegetation were dug out of the canals twice a year. third, a complex system of rice husbandry was used in which the rice fields were ploughed, manured, and subjected to a program of alternate drying and flooding. consequently, neither the canal system nor the rice fields contained much in the way of snail habitats. snails were confined to temporary pool sites, filled with rain or seepage water. all these schemes were built on land with an appreciable slope and with relatively porous soils. even when irrigation was in progress, the field canals were not always in use and dried out rapidly. while snails are often able to withstand limited periods of drought, it is unlikely that any large snail populations could develop under these conditions in any one season. furthermore, on five of these schemes, field canals were often re-routed from season to season so that the establishment of suitable snail habitats was rendered even more unlikely. mobarak (1982) reported that after 1970 prevalence of urinary schistosomiasis in upper egypt reversed a previous downward trend and began to increase again because of the shift from basin to perennial irrigation. however, in any case, increased use of parenteral antischistosomal therapy (pat, injections of antimony-based drugs) was bringing schistoso miasis under control in egypt. in the northern part of upper egypt, prevalence dropped from 29.4% in 1977 to 11.5% in 1983, while further south, prevalence reportedly fell from 26. 4% in 1980 4% in to 16% in 1983 4% in (who, 1985 . most experts agreed that applying the proper combination of sanitary engi neering, water control management, snail control, infection surveillance, and treatment drugs can avert adverse effects of irrigation on schistosomiasis. moreover, there was an impres sion that even without water control measures and environmental sanitation, chemotherapy with or without treat ing water to kill snails would adequately control schistosomiasis transmission. fenwick (1989) noted that in the newer rahad irrigation scheme, east of the gezira plain in the sudan, because of the use of drugs and snail control, the incidence of schistosomiasis remained very low, despite very poor sanitary conditions. it was predicted, however, that relax ing control measures would cause a surge in schistosomiasis. although oral drugs started to be used in egypt in the 1970s, pat use continued into the mid-1980s. praziquantel, which also has a high cure rate for s. mansoni, became available in egypt in 1982 and has been the treatment of choice there since the late 1980s. although the massive pat campaigns were successful in strongly reducing disease incidence, a study by frank et al. (2000) concludes that the intensity, widespread geographical coverage, and duration of the campaigns, together with unsafe injection practices (inappropriate sterilization pro cedures), have been responsible for the nationwide spread of hepatitis c in egypt in recent decades. the authors state that the enormous dimension of egypt's schistosomiasis problem and the sheer size of the antischistosomiasis effort, combined with the characteristics of pat, provided an effective mechanism for a massive increase and establishment of hepatitis c virus in the egyptian population. according to these authors, this is "the world's largest iatrogenic transmission of blood-borne patho gens known to date." moreover, it is probable that the heavy reliance on an effective chemical treatment also allowed the continuation of water management schemes that were contri buting to the maintenance of large numbers of snails in aquatic environments. the evolution of the schistosomiasis problem in egypt and sudan described above highlights the importance of developing water management programs able to keep vector proliferation under control. this lesson is also highly relevant to the construction of large-scale reservoirs and irrigation facil ities as in the case of the three gorges dam. in israel, biomphalaria alexandrina was eradicated through a combination of factors including chemical applications. as in all cases, snails return some time after the application of mol luskicides. some combined measures used for the control of snail vectors have been successful, such as increasing water currents to over 20 cm s −1 , rapid emptying and drying up of water reservoirs, and weekly deflection of infested water courses along different routes (saliternik, 1979) . as stated previously, the success of chemotherapy in treating this disease and of molluskicides for eradicating snails does not imply that preventive measures should not be taken for avoid ing vector proliferation based on knowledge of their ecohydrological setting. all vector snails require water, at least for breeding. the management of water bodies is therefore a potentially powerful control method. for example, in the case of rice cultivation there are opportunities for vector control by changing the aquatic habitat of the snail in a way compatible with maximum crop production. infection of humans mostly takes place not in the rice field itself, but in irrigation canals and surrounding living quarters. different hydrological and rice husbandry approaches have been used in various countries. however, generalizations should be made with care because each snail species has its own preferences and tolerances regard ing shade, water velocity, the steepness of canal walls, and drought tolerance. rice cultivation by itself can be used as an environmental method of snail control in that it brings about ecological changes that can reduce snail habitat. the philippines has promoted more intensive scientific methods of rice cultivation to control schistosomiasis (hairston and santos, 1961) . snail control is achieved at different stages of rice growing in a number of different ways, for example, by deep plowing, which turns over the soil and buries the snails; or by draining the ricefield at harvest and keeping it dry until the next crop, which kills the snails and prevents them from breeding. in japan, s. japonicum eradication was accomplished by treatment, sanitation, control of animal reservoir host, educa tion, and elimination of most of the snail colonies (garcia, 1988) . the steepness of the walls of irrigation channels was increased and later they were lined with concrete and main tained clear of silt, vegetation, and debris to supplement the eradication of snails in the ricefields, which resulted from intensive cultivation. extensive rice-growing areas in china's mainland have been cleared of oncomelania snails (garcia, 1988) . the measures taken have included digging new water channels parallel to the existing snail-infested streams and using the excavated soil to fill the old ones, clearing streambeds, and removing vegetation. where the soil structure permits, the banks have been made steeper. in the philippines, similar measures have been taken as in china; in addition, converting undrainable swampy areas into fishponds and improving agricultural prac tices have successfully controlled snails in limited areas. thus, an integrated approach to drainage problems can result in increased production while reducing health risks. in the ecohydrology approach, it is essential to consider the whole basin in management policies, especially when a disease agent can be transmitted by different species of the same host (in this case a snail) that is differentially distributed along altitude gradients in river basins. both b. truncatus and planorbarius metidjensis are intermediate hosts of s. haematobium in southwestern morocco. a basin investigation (yacoubi et al., 2007) in five rivers identified sites colonized by these species and compared the habitats in which they were found. the p. metidjensis was observed in the upper valleys of three rivers, whereas b. truncatus was found in sites of lower altitude. a component analysis demonstrated that altitude (from 4 to 1380 m), water ph (from 5.9 to 9.2), and electric conductivity (from 120 to 6020 μs cm −1 ) were the main descriptors of environment. the p. metidjensis was associated to high altitude and low electric conductivity. however, b. truncatus was asso ciated to being found in lower altitude sites with medium electric conductivity in water. it has been mentioned above that periodic canal or field drying had been used successfully for snail control. nevertheless, before a control plan is adopted and implemen ted, the effects of drying out have to be monitored and thoroughly understood for each snail species: snails that are capable of undergoing diapause can circumvent unfavorable environmental conditions, including long periods of drought. cooper et al. (1992) found that diapause influenced the sus ceptibility of biomphalaria glabrata snails to s. mansoni infection. juvenile snails exposed just prior to diapause, or immediately following a diapause period of 3 weeks, were highly susceptible to infection by s. mansoni miracidia. however, snails that underwent diapause produced compar able or only slightly fewer cercariae than did nondiapausing snails. these studies indicate that diapause in b. glabrata does little to decrease a snail's ability to act as an intermediate host for s. mansoni or to interrupt the development of the parasite. for these reasons, great attention should be given to diapausing snail populations when planning programs for mollusk control. thus, for snail control, it is important that not only the agricultural field but also irrigation and drainage channels, as well as the water source, be considered part of the agroecosys tem. this parallels the ecohydrology approach that considers the whole basin, from the river source to the wetlands, estuar ine, and coastal zone as an integrated management unit. both agricultural and ecohydrological models should converge in a new synthesis integrating their own tools with practices based on traditional knowledge, socioeconomical cost-benefit analysis of vector eradication, and agri-and/or aquacultural production. the type of wetland management approach, particularly when restoration or creation is planned, will require previous surveys of the mosquito species and their habitat types, locally and at basin level. in the following sections, we present a summary of main species/habitat combinations for different hydrological settings extracted from anonymous (2009b) . relatively few mosquito species breed in running waters, such as streams. larvae can be flushed out when stream volume increases, and to remain in the stream requires a large amount of energy. the tropical genus, chagasia, and some anopheles species are stream breeders. stream breeders will find vegeta tion along banks with which to anchor themselves or attempt to remain away from the main flow of the stream by seeking isolated eddies. transient water sources, such as flooded areas and ditches, are used as breeding grounds for species whose eggs can with stand desiccation and whose life cycles require alternating periods of wet and dry, such as aedes and psorophora. the quality of transient water changes with time, which can result in a succession of different species using the same pool. transient waters include woodland pools created by spring rains (aedes stimulans), fresh floodwater (aedes canadensis), and tidal floodwater (aedes sollicitans). permanent or semipermanent waters support characteristic aquatic vegetation. cattail, rushes, and sedges are typical fresh water swamp vegetation. genera associated with permanent water are anopheles, culex, culiseta, coquillettidia, and uranotaenia, whose eggs are not desiccant resistant and must be laid directly on the water. aedes adults will oviposit near the edge of the swamp, or within tussocks of vegetation, requiring later flooding of the eggs for hatching. as with transient waters, there are seasonal changes in the vegetation, water quality, and mosquito species present. permanent waters can include fresh water swamps, such as, for example, tussock (aedes abserratus) or cattail swamps (coquillettidia perturbans), as well as brackish water swamps with salt marshes (culex salinarius). besides nat ural environments, polluted water with floating debris can be a habitat for species such as culex pipiens. container water habitat can be found in both natural set tings, such as water held by plants to artificial settings and water found in tires. container water is characteristically clear and many container species now also use artificial sites as they provide insulation against the weather and are more numerous (aedes aegypti and aedes albopictus). increasing dengue incidence in not only tropical but also subtropical countries requires a thorough elimination of such urban, man-made microhabitats. there are various techniques for mosquito control based on different principles. all involve modification of the hydrologi cal setting, ranging from total wetland drainage to an increase in their tidal flooding. a summary of these methods, including parallel grid ditching, open marsh water management, and runneling, is presented in the following paragraphs. parallel grid ditching consists in the physical removal of water from intertidal marshes and was one of the first largescale forms of mosquito control (lesser (2007) ; figure 16 ). parallel grid ditches were dug in salt marshes, spacing these ditches about 45 m apart to remove standing surface water where mosquitoes might breed. extensive ditching programs for mosquito control in north america were only moderately effective, since many breeding potholes were not drained dry, and there were long-term nega tive effects on wildlife and salt-marsh ecosystems. many nonmosquito breeding wetlands that provided wildlife habitat were unnecessarily drained and salt-marsh vegetation commu nities were changed into fragmented wetlands. birds were particularly affected through the draining of larger natural ponds. by the early 1960s, there was an increasing awareness of wetland values and functions, and the value of parallel grid ditching was questioned. understanding of the drawbacks of the parallel grid-ditching technique led to the development of a new mosquito control source-reduction technique called open marsh water manage ment (omwm). it started in the late 1960s and was further optimized until the early 1980s. the goals of omwm are: (1) control of salt-marsh mosquitoes; (2) reduction of insecti cide applications; and (3) habitat enhancement for salt-marsh fish and wildlife (ferrigno and jobbins, 1968; hruby et al., 1985) . the omwm method involves the selective installation of small, shallow ponds and interconnecting ditches superim posed on known mosquito-breeding habitats ( figure 17 ). this aims to eliminate wet-dry-wet cycles necessary for determined species and any newly created permanent water habitats are unattractive for mosquito egg deposition. this simultaneously improves habitats for mosquito-eating larvivorous fishes which can quickly invade, via tidal flooding, any newly created omwm pond or ditch. scattered mosquito breeding depressions and sheetwater habitats are connected through pond and ditch excavations to allow unimpeded water flow and predatory fish movement, while isolated potholes are often filled with natural soils to eliminate these smaller-sized breeding depressions (lesser, 2007 ; figure 17 ). the increase of tidal inundation frequency and predation by fish significantly reduce mosquito density. runneling is an effective method for controlling mosqui toes that breed in intertidal salt marshes through a type of habitat modification using shallow channels. this technique is based on omwm principles (wolfe, 1996) . it increases tidal frequency to a marsh and removes surface sheet water from low-lying areas high on the marsh. runnels are linked to the tidal source, promoting tidal exchange between graded regions of the marsh. they are conceived to allow transport of lowamplitude tides to areas of salt marsh in a way so that pools do not form, even after spring tides. runnels are shallow figure 17 the omwm system, involving the selective installation of small, shallow ponds and interconnecting ditches superimposed on known mosquito-breeding habitats. (<30 cm deep) spoon-shaped channels constructed along nat ural drainage lines on the salt marsh ( figure 18 ) to a maximum gradient of 1:1000 (hulsman et al., 1989) . due to the slight slope, runnels enable slow water movement even during lowamplitude tides. the net result is a reduction in mosquito breeding areas, the modification of pools and edges for egg conditioning (the process involving flooding and drying events that prepares mosquito eggs for hatching), and larval development. there are few apparent negative impacts at the modified site (hulsman et al., 1989; dale and hulsman, 1990; dale et al., 1993; latchford, 1997) . further, like omwm, they allow water to drain from trap pools and permit predatory fish to gain access to the mosquito larvae, at least during high tide. in comparison to grid ditching and omwm, runneling is an environment-oriented approach to salt-marsh management for mosquito control that aims to alter the salt marsh as little as possible, while causing significant reductions in mosquito numbers. the main difference between the three approaches lies in the magnitude of the habitat modification. ditching involves the greatest alteration to the marsh, and runneling the least. runneling has a lesser effect on the estuarine environ ment as a whole than does either ditching or omwm. 10.12.5 conclusions 10.12.5.1 some reflections on dams, water scarcity, ecohydrology, and health although the construction of reservoirs is controversial, the rising demand for water by an increasing human population makes more dams inevitable (jobin, 1999) . in a review, morley (2007) calls attention of the fact that most parasitological studies in relation to reservoir construction have been focused on schistosomiasis and other tropical diseases of humans (stanley and alpers, 1975; jobin, 1999) . in comparison, the impact of reservoir construction on indigenous aquatic parasite fauna of wildlife has been a subject largely ignored by the scientific community. however, reservoir formation can have profound effects on the parasite fauna of fish, birds in the reservoir, as well as up-and downstream of it. changes in host-parasite relationships and switches between animal and human hosts can occur (morley, 2007 and references therein) . the role of parasites in environmental monitoring is increas ingly recognized (lafferty, 1997; lafferty and kuris, 2005) . thus, the surveillance of the effects of reservoirs on parasite fauna of aquatic wildlife may provide important general infor mation on both short-and long-term changes that occur within and downstream of new reservoirs during the maturation pro cess of the reservoir. the above-described cases that show the effect of dam con struction on onchocerciacis and schistosomiasis call attention to the need to evaluate changes in flow power and velocity downstream of proposed dams, in order to assess their likely health impact. ecohydrological measures are required to improve the operation of existing dams to provide more effective control of disease vectors (see section 10.12.2.2.3). the modeling of the effect of controlled flooding pulses on the plankton dynamics in the guadiana estuary (wolanski et al., 2006) is an outstanding example of the potential of the appli cation of ecohydrological principles for the control of toxic algal blooms. in arid and semiarid regions, the quality of water in artificial reservoirs is essential to human health, particularly in climati cally unstable regions. for example, recent el niño/la niña-southern oscillation teleconnections have produced a pro longed drought of ∼3 years in south argentina. this has interrupted a period of about 30 years of rainfall significantly above the historical average and produced a decline to critical levels in the reserves of drinking water reservoirs, which like other water bodies in the region, have suffered from recurrent summer algal blooms (kopprio et al., 2008) . however, the perception that cyanobacteria can represent a threat to human health only in connection with acute events such as blooms should be widened to consider the possibility of neurologic damage as consequence of chronic exposition to toxins such as bmaa via long-term ingestion of water or aquatic fauna. this should be taken into account when developing schemes for preventing cyanobacterial blooms by manipulating natural predator communities. the reduction of the nutrient load input to the water reservoir probably remains the best preven tive measure to prevent harmful algal blooms. water treatment should be regularly checked and improved to remove the organisms and their toxins from drinking-water supplies, where appropriate. water treatment by flocculation and sedi mentation, followed by sand filtration, is supposed to remove live cyanobacterial cells and debris. however, there is evidence that plants that are not working properly can actually increase cell counts of algae with potential toxicity (in this case, anabaena circinalis and microcystis aeruginosa) in the treated water (echenique et al., 2006) . throughout this chapter, examples have been referred to of actual and potential conflicts of interest between alternative uses of aquatic systems, for example, between the desire to restore degraded wetlands and the need to protect health of the human population living nearby. a relevant example of policy conflicts in an industrialized country is the experience of the tennessee valley authority (tva), where health concerns in the past gave rise to management measures that conflict with modern recreational interests (bos, 1999) . the meeting report of the ninth meeting of the who/fao/united nations environment programme (unep) panel of experts on environmental management for vector control in 1989 includes the following passage: as national and regional priorities change, so do policies, and there must therefore always be a provision for their reconsideration and modification. sometimes, though, the acute problems that led to the original priority setting might have become latent rather than have disappeared completely, and while public awareness and political pressure favour a policy change, the original goals of such policies should not be ignored. this was well illustrated by the water man agement policies including mosquito control established by the tva in the 1930s. the standards of mosquito control maintained by tva equalled those maintained in privately owned river impoundments under prevailing public health regulations. the measures included the programmed fluctuation of water levels in the reservoirs, a practice that played a key role in reducing anopheles populations and eradicating malaria transmission from the valley. new uses of the reservoirs, including recreation and the promotion of nature conservation had led to a conflict of interests. for recreation, stable water levels during summer and early autumn were required; con servation of certain fish species and of waterfowl required higher water levels in spring to promote fish spawning and the rapid growth of aquatic vegetation for the fowl. such changes in water manage ment regimes would without doubt result in increased mosquito populations, yet the potential risk for the reintroduction of vectorborne disease was not appreciated after three generations of malaria free experience. in recent years much interest has been directed towards the protection and establishment of wetlands, without pay ing sufficient attention to their mosquito breeding potential. consequently, tva has been faced with a conflict of new policy directives concerning wetlands, existing mosquito control policies and state regulations for impounded water. the use of constructed (artificial) wetlands for the treatment of domestic waste water and its processing for reuse is of particular concern, since these could pro duce large quantities of potential disease vectors and they are often sited close to populated areas (peem/who, 1991: 17-18). this stresses the necessity of harmonizing policies of reservoir management for vector control with other policies concerned with land use patterns, to ensure that areas of potential risk, such as artificial wetlands, are planned away from areas of human habitation. presently we face a complex environmental situation that seems to be changing at a much faster rate than our current capacity to revise and renew our intellectual schemes or to generate integrated management structures capable to enhance both ecosystem and human health. take, for example, the case of influenza virus. the loss of wetlands around the globe may force many wild birds onto alternative sites like farm ponds and paddy fields, bringing them into direct contact with domestic fowl and humans and providing greater opportu nities for the spread of the h5n1 virus (anonymous, 2006) . poor planning in response to development pressures has led to the increasing loss or degradation of wild ecosystems which are the natural habitats for wild birds. the displaced wild birds increasingly seek to feed and live in areas populated by domestic poultry and humans. thus, wetland creation must also consider these factors, since they will attract migratory birds if located near their routes. despite this being considered an enrichment of landscape ecology in terms of diversity, recreational value, landscape beauty, etc., the risk of increasing transmission of emerging diseases must be dispassionately considered. an increase in biodiversity does include not only those species humans like, but also the diversity of vectors capable of transmitting diseases. the distance of the wetlands to be created from populated centers, the direction of prevail ing winds, and other transport mechanisms should be carefully taken into account. this issue of 'ecohealth' highlights the interplay between agriculture, animal (domestic and wildlife) and human health, the integral health of aquatic ecosystems, and sociocultural factors. nutrient reduction in wastewaters or surface waters is a priority for reducing risks to human health, as well as for the reduction of disease vectors in surface waters. exploration of phytotechnologies relying on direct belowground absorption of nutrients by plant root biomass could provide alternatives to construction of open wetlands in places where this might involve disease vector proliferation. the role of lymnaea auricularia (linnaeus) and lymnaea peregra (müller) (gastropoda: pulmonata) in the transmission of larval digeneans in the lower thames valley background state leading to arsenic accumulation in the bengal basin groundwater what is their actual role in the spread of the virus? mangrove management and conservation a review of avian influenza in different bird species problems and effects of schistosomiasis in irrigation schemes in the sudan regulation and stability of host-parasite population interactions. i. regulatory processes brazilian spotted fever: a case series from an endemic area in southeastern brazil. epidemiological aspects the human waste. a report by wateraid and tearfund what is their actual role in the spread of the virus river blindness in west africa is nearly eradicated, canada is key donor to expansion efforts across africa cholera, not gastroenteritis hits mirpur khas. the nation larval habitats of mosquitoes a pesquisa em esquistossomose no brasil. modernos conhecimentos sobre esquistossomose mansônica host densities as determinants of abundance in parasite communities epidemic of diarrhea caused by vibrio cholerae non-o1 that produced heatstable toxin among khmers in a camp in thailand effects of increasing organic matter loading on the dissolved o 2 , free dissolved co 2 and respiration rates in the piracicaba river basin, southeast brazil production of the neurotoxin bmaa by a marine cyanobacterium the volta river basin. comprehensive assessment of water management in agriculture. comparative study of river basin development and management exposure to schistosoma mansoni infection in a rural area in brazil. part iii: household aggregation of water-contact behaviour water resources development and health: the policy perspective seasonal and interannual cycles of endemic cholera in bengal 1891-1940 in relation to climate and geography surveillance for waterborne-disease outbreaks -united states distribution of insecticide-treated bednets during an integrated nationwide immunization campaign-togo pathogenic vibrios in the natural aquatic environment cholera in calcutta: some observations of epidemiological interest and the problem of its control the global status of schistosomiasis and its control cyanobacterial toxins: risk management for health protection temporal changes of mangroves vegetation boundaries in amazonia: application of gis and remote sensing techniques vulnerability to coastal cholera ecology marine ecosystems and cholera global climate and infectious disease: the cholera paradigm viable but non-culturable vibrio cholerae and related pathogens in environment: implications for release of genetically engineered microorganisms vibrios in the environment: viable but non-culturable vibrio cholerae reduction of cholera in bangladeshi villages by simple filtration schistosoma mansoni infection in diapausing biomphalaria glabrata snails: studies of temperature and genetic influences on diapausing behavior epidemiological and control aspects of schistosomiasis in brazilian endemic areas. memorias do instituto oswaldo cruz epidemiological study on mansoni schistosomiasis in irrigation areas of northeastern brazil biomagnification of cyanobacterial neurotoxins and neurodegenerative disease among the chamorro people of guam diverse taxa of cyanobacteria produce β-n-methylamino-l-alanine, a neurotoxic amino acid the parasitism of schistosoma mansoni (digenea-trematoda) in a naturally infected population of water rats, nectomys squamipes (rodentia-sigmodontinae) in brazil runneling to control saltmarsh mosquitoes: long-term efficacy and environmental impacts a critical review of salt marsh management methods for mosquito control london's 'great stink' and victorian urban planning global maps of atmospheric nitrogen deposition, 1860, 1993, and 2050. data set from oak ridge national laboratory distributed active archive center the role of ecotones in emerging infectious diseases models for multi-species parasite-host communities influenza drinking water: problems related to water supply in bahía blanca key issues in the safe use of wastewater and excreta in aquaculture algal blooms in the spread and persistence of cholera climate and health rickettsiae detection in amblyomma ticks (acari: ixodidae) collected in the urban area of campinas city domestic ducks could pose a new avian influenza threat. joint fao, oie and who warning 11 changing epidemiology of cholera due to vibrio cholerae 01 and 0139 bengal in dhaka seasonal epidemics of cholera inversely correlate with the prevalence of environmental cholera phages emergence and evolution of vibrio cholerae o139 irrigation in the sudan and schistosomiasis open marsh water management land use and nitrogen export in the piracicaba river basin volta basin research project [vbrp]. remediation of the environmental impacts of the akosombo and kpong dams the role of parenteral antischistosomal therapy in the spread of hepatitis c virus in egypt ecological impact on the status of otter (lutra-perspicillata) nitrogen cycles: past, present, and future vector-borne disease control in humans through rice agroecosystem management. international rice research institute. who/fao/unep panel of experts on environmental management for vector control bangladesh: wo der klimawandel nach salz schmeckt the relationship between primary aluminum production and the damming of world rivers. irn working paper 2. international rivers network (irn) endemic cholera in rural bangladesh atypical fulminant rickettsia rickettsii infection (brazilian spotted fever) presenting as septic shock and adult respiratory distress syndrome human schistosomiasis study on schistosomiasis control strategy in ertan reservoir ecology drives the worldwide distribution of human diseases sugar cane industry as a source of water pollution -case study on the situation in ipojuca river environmental impacts of the akosombo dam and effects of climate change on the lake levels ecological control of the snail host of schistosoma japonicum in the philippines coastal schemes and the ksdp the effect of rainfall on the incidence of cholera in bangladesh severe hepatotoxicity caused by the tropical cyanobacterium (blue-green alga) cylindrospermopsis raciborskii (woloszynska) seenaya and subba raju isolated from a domestic water supply reservoir wasserversorgung und abwasserentsorgung von megacities. fachabteilung für hydrologie und wasserwirtschaft predisposition to urinary tract epithelial metaplasia in schistosoma haematobium infection nitrogen use in the united states from 1961 to 2000 and potential future trends open marsh water management in massachussetts: adapting the technique to local conditions and its impact on mosquito larvae during the first season the ecology of wildlife diseases the runneling method of habitat modification: an environment-focused tool for salt marsh mosquito management vibrios in marine and estuarine environment west nile virus infection in arthropods return of the cycad hypothesis -does the amyotropic lateral sclerosis/parkinsonism dementia complex (als/pdc) of guam have new implications for global health? ipcc technical guidelines for assessing climate change impacts and adaptations. part of the ipcc special report to the first session of the conference of the parties to the un framework convention on climate change an assessment of the intergovernmental panel on climate change: synthesis report summary for policymakers pakistan: focus on poisoned water and disabilities. integrated regional information networks as part of the un office for the coordination of humanitarian affairs (ocha) faecal contamination of drinking water sources of dhaka city during the 2004 flood in bangladesh and use of disinfectants for water treatment probable role of blue-green algae in maintaining endemicity and seasonality of cholera in bangladesh: a hypothesis confronting the realities of wastewater used in agriculture ecological study of vibrio cholerae in vellore dams and disease dams in china and africa have been linked to positive health impacts in their local population influence of eutrophication on disease in aquatic ecosystems: patterns, processes, and predictions the challenge of the megacities. the new york times bird migration routes and risk for pathogen dispersion into western mediterranean wetlands women and water: issues of entitlements, access and equity. in: pakistani women in context, a companion volume to pakistan country gender assessment adsorption of vibrio parahaemolyticus onto chitin and copepods trinkwasserversorgung in megastädten: das beispiel calcutta, indien the national campaign for the treatment and control of bilharziasis from the scientific and economic aspects on the history of the anti-bilharzial campaign in the dakhla oasis mechanisms controlling the chemical composition of lakes and rivers: data from africa black flies: ecology, population management, and annotated world list regulation of zooplankton biomass and production in a temperate, coastal ecosystem. 1. copepods 1884. an address on cholera and its bacillus effects of climate change and eutrophication on the natural reserve laguna chasicó, a coastal brackish lake of argentina. proceeding of the ecsa 44 science and management of estuaries and coast: a tale of two hemispheres ecology of rickettsia in south america rickettsia species infecting amblyomma cooperi ticks from an area in the state of sao paulo, brazil, where brazilian spotted fever is endemic environmental parasitology: what can parasites tell us about human impacts on the environment? parasitism and environmental disturbances tropenmedizin in klinik und praxis sediment porewater salinity and mangrove vegetation height in bragança, north brazil: an ecohydrology-based empirical model influence of estuarine dynamics and catastrophic climatic events on vibrio distribution in the karnaphuli estuary implications of mangrove dynamics for private land use in bragança, north brazil: a case study the effectivness and environmental impacts of runneling, a mosquito control technique open marsh water management: a source reduction technique for mosquito control effects of global climate on infectious disease: the cholera model climate and infectious disease: use of remote sensing for detection of vibrio cholerae by indirect measurement predictability of vibrio cholerae in chesapeake bay environmental signatures associated with cholera epidemics bilharziasis control in pump schemes near khartoum, sudan, and an evaluation of the efficacy of chemical and mechanical barriers effect of the aswan high dam on prevalence of schistosomiasis in egypt the role of birds in the ecology of west nile virus in europe and africa a short introduction -what is schistosomiasis? possible waterborne transmission and maintenance of influenza viruses in domestic ducks expansion of sugarcane ethanol production in brazil: environmental and social challenges sources of reactive nitrogen affecting ecosystems in latin america and the caribbean: current trends and future perspectives macro-epidemiologic aspects of schistosomiasis mansoni: analysis of the impacts of irrigation systems on the spatial profile of the endemic in bahia plankton richness in a eutrophic reservoir parasitic and infectious disease responses to a changing global nitrogen cycle chitin induces natural competence in vibrio cholerae natural infection with zoonotic subtype of cryptosporidium parvum in capybara (hydrochoerus hydrochaeris) from brazil overwhelming watery diarrhoea associated with cryptosporidium in an immunosuppressed patient floods and public health consequences, prevention and control measures co occurrence of β-n-methylamino-l-alanine, a neurotoxic amino acid with other cyanobacterial toxins in british waterbodies cholera and estuarine salinity in calcutta and london response of toxigenic vibrio cholerae 01 to stresses in aquatic environments cholera epidemiology in developed and developing countries: new thoughts of transmission, seasonality, and control the impact of physico-chemical stress on the toxigenicity of vibrio cholera diversion of the ganges water at farakka and its effects on salinity in bangladesh the schistosomiasis problem in egypt anthropogenic effects of reservoir construction on the parasite fauna of aquatic wildlife the role of bithynia tentaculata in the transmission of larval digeneans from a gravel pit in the lower thames vally a mechanism for slow release of biomagnified cyanobacterial neurotoxins and neurodegenerative disease in guam toxin profiles of vibrio cholerae non-o1 from environmental sources in calcutta national institute of cholera and enteric diseases, calcutta: annual report. indian council of medical research acute enterocolitis in a human being infected with protozoan cryptosporidium the public health consequences of disasters clean coastal waters: understanding and reducing the problems of nutrient pollution global patterns of influenza a virus in wild birds schistosomiasis in the sudan: historical background and the present magnitude of the problem water that we drink in sindh distribuição dos caramujos no brasil. modernos conhecimentos sobre esquistossomose mansônica no brasil report of the ninth meeting of the joint who/fao/unep panel of experts on environmental management for vector control (peem) avaliação por fotointerpretação o das áreas de abrangência dos diferentes estados da erosão acelerada do solo em canaviais e pomares de citros fatal microcystin intoxication in haemodialysis unit in caruaru world population data sheet estimating the global burden of disease from water, sanitation and hygiene at a global level effects of temperature and salinity on vibrio vulnificus population dynamics as assessed by quantitative pcr rickettsiosis as paradigms of new or emerging infectious diseases migratory birds and spread of west nile virus in the western hemisphere birds, migration and emerging zoonoses: west nile virus, lyme disease, influenza a and enteropathogens from shakespeare to defoe: malaria in england in the little ice age the vibrio shiloi/oculina patagonica model system of coral bleaching cholera seasonality in madras (1901-1940): dual role for rainfall in endemic and epidemic regions a history of land use in arid regions the specific methods of control and eradication of schistosomiasis in israel the fossil record: tracing the roots of the cyanobacterial lineage the incidence and distribution of the human schistosomes in egypt on the dominance of filamentous cyanobacteria in shallow, turbid lakes cholera in a developing megacity effect of climate change on sea water intrusion in coastal aquifers consecutive outbreaks of vibrio cholerae o139 and v. cholerae o1 cholera in a fishing village near karachi effects of temperature and salinity on vibrio cholerae growth low nitrogen to phosphorus ratios favour dominance by blue-green algae in lake phytoplankton man-made lakes and human health providing health services on the aswan high dam the development of irrigation and its influence on the transmission of bilharziasis in tanganyika distribution of the snail biomphalaria glabrata, intermediate host of schistosoma mansoni, within a st. lucian field habitat chitin degradation proteins produced by the marine bacterium vibrio harveyi growing on different forms of chitin protection of sudanese irrigations workers from schistosome infections by a shift to earlier working hours a parasitological and malacological survey of schistosomiasis mansoni in the beles valley, northwestern ethiopia biodiversity of vibrios. microbiology and in malaria war, south africa turns to pesticide long banned in the west resource competition and community structure human health effects of a changing global nitrogen cycle evaluation of total phosphorus as a predictor of the relative biomass of blue-green algae with emphasis on alberta lakes guidelines for the integrated management of the watershed -phytotechnology and ecohydrology -newsletter and technical publications fast melting glaciers from rising temperatures expose millions in himalaya to devastating floods and water shortages competition for water resources of the volta basin vibriosis in shrimp aquaculture capybaras on an anthropogenic habitat in south eastern brazil disease stalks new megacities. guardian effect of fecal pollution on vibrio parahaemolyticus densities in an estuarine environment water insecurity and the poor: issues and research needs. zef discussion paper who, geneva. who, 1993. the control of schistosomiasis: second report of the who expert committee strategy to rollback malaria in the who european region climate change and health: impact and adaptation water-related diseases water-related diseases water-related diseases: japanese encephalitis water, sanitation and hygiene links to health the world health report schistosomiasis fact sheet n°115 quantifying environmental health impacts about the public health mapping and gis programme temporal occurrence of vibrio species and aeromonas hydrophila in estuarine sediments ecohydrology as a new tool for sustainable management of estuaries and coastal waters an ecohydrology model of the guadiana estuary (south portugal) water and human security effects of open marsh water management on selected tidal marsh resources: a review ending african river blindness: entomologist vincent resh has leveraged science and diplomacy to help bring an epidemic under control along 30,000 miles of west african rivers. breakthroughs magazin, college of natural resources geographical distribution of schistosomes and their intermediate hosts. epidemiology and control of schistosomiasis (bilharziasis) overview of disease fact sheets habitats of bulinus truncatus and planorbarius metidjensis, the intermediate hosts of urinary schistosomiasis, under a semiarid or an arid climate factors affecting the prevalence of schistosomiasis in the volta region of ghana ecohydrology -the use of ecological and hydrological processes for sustainable management of water resources impact of the three gorges dam construction on transmission of schistosomiasis in the reservoir area relationship between the transmission of schistosomiasis japonica and the construction of the three gorge reservoir 