# bib

id: cord-255971-kamai25b
author: Wee, Liang En
title: Reduction in healthcare-associated respiratory viral infections during a COVID-19 outbreak
date: 2020-07-03
extension: .txt
mime: text/plain
words: 295
sentence: 13
flesch: 32
cache: cache/cord-255971-kamai25b.txt
txt: txt/cord-255971-kamai25b.txt
summary:
  However, the effectiveness of infection control during a 45 COVID-19 outbreak on healthcare-associated RVI has yet to be assessed. [1] Infection prevention bundles comprising segregation of 41 symptomatic patients, droplet/ contact precautions and visitor screening can potentially reduce the 42 transmission of RVI on high-risk units, [2] though hospital-wide implementation has been limited.


id: cord-275068-yr076sl6
author: Ayoub, Fares
title: Football and COVID-19 risk: correlation is not causation
date: 2020-09-03
extension: .txt
mime: text/plain
words: 447
sentence: 12
flesch: 34
cache: cache/cord-275068-yr076sl6.txt
txt: txt/cord-275068-yr076sl6.txt
summary:
  [5] Low vitamin D levels have often been associated with a 16 higher risk of infections, but vitamin D supplementation has not been shown to prevent respiratory 17 1 impact journals during the pandemic, but it is important to remember that correlation does not equal 2 causation. A patients had a higher risk 9 of severe COVID-19 compared to other blood types,[3] while other studies have found associations 10 between vitamin D levels/latitude, and Bacille de Calmette et Guérin (BCG) vaccine and mortality to 11 COVID-19.


id: cord-322585-5gio6ruj
author: Lanari, Marcello
title: Children and SARS-CoV-2 infection: innocent bystanders…until proven otherwise
date: 2020-06-25
extension: .txt
mime: text/plain
words: 441
sentence: 12
flesch: 31
cache: cache/cord-322585-5gio6ruj.txt
txt: txt/cord-322585-5gio6ruj.txt
summary:
  Paediatric inflammatory multisystem 163 syndrome and SARS-CoV-2 infection in children -15 Angiotensin-converting enzyme in developing lung and 165 kidney A crucial role of angiotensin converting 167 enzyme 2 (ACE2) in SARS coronavirus-induced lung injury Evolution of the immune system in humans from 169 infancy to old age Prevalence of human coronaviruses in 171 adults with acute respiratory tract infections in Beijing Review article: gastrointestinal features in COVID 19 and the 173 possibility of faecal transmission Children are unlikely to be the main drivers of the COVID-19 pandemic -a 175 systematic review School closure and 177 management practices during coronavirus outbreaks including COVID-19: a rapid systematic 178 review A Case Series of children with 2019 novel 180 coronavirus infection: clinical and epidemiological features further studies are needed [10] . The possible and different explanations for understanding why the infection seems to be more benign and less frequent in children are discussed.


id: cord-256853-2s31fn04
author: Jin, Cheng Cheng
title: Correlation between viral RNA shedding and serum antibodies in COVID-19 patients
date: 2020-05-23
extension: .txt
mime: text/plain
words: 325
sentence: 15
flesch: 44
cache: cache/cord-256853-2s31fn04.txt
txt: txt/cord-256853-2s31fn04.txt
summary:
  [2] Based on currently available information, the relationship between the 6 dynamic of serum antibodies and viral replication is unclear. In this study, we 7 investigated the correlation between serum antibodies and duration of viral RNA 8 shedding.


id: cord-331002-7uojryqz
author: Valent, Francesca
title: Detection of SARS-CoV-2 in nasopharynx according to clinical phenotype of affected patients
date: 2020-09-06
extension: .txt
mime: text/plain
words: 785
sentence: 38
flesch: 50
cache: cache/cord-331002-7uojryqz.txt
txt: txt/cord-331002-7uojryqz.txt
summary:
  Coronavirus disease 2019 (COVID-19) situation report: 28 Laboratory testing for coronavirus disease (COVID-19) in suspected 209 human cases Clinical Course of Patients Infected With SARS-CoV-2 in Singapore Clinical course and risk factors for mortality of 215 adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study SARS-CoV-2 Viral Load in Upper 218 Respiratory Specimens of Infected Patients Early risk factors for the duration of 220 SARS-CoV-2 viral positivity in COVID-19 patients The early phase of the 223 COVID-19 outbreak in Viral 226 Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome 227 Viral Load Kinetics of MERS 229 Duration for carrying SARS-CoV-2 in COVID-19 231 patients Difference Is Associated With Severity of Coronavirus Disease 2019 After adjusting for sex and age, at any 129 time point, ICU patients were less likely to return to negativity than the other patients.


id: cord-008258-5v55vv4s
author: Raoult, D.
title: Is it the end of the nervous breakdown on avian influenza?
date: 2015-06-21
extension: .txt
mime: text/plain
words: 598
sentence: 24
flesch: 53
cache: cache/cord-008258-5v55vv4s.txt
txt: txt/cord-008258-5v55vv4s.txt
summary:
  In total the zoonotic variant of H5N1 avian flu and H9N2 is very common in people in contact with poultry; it is banal and most of the time, asymptomatic. This current work [2] has just confirmed what was noted for several years but had been denied, which is the high occurrence of asymptomatic infection in people who are in contact with infected poultry.


id: cord-288425-po35m6d9
author: Albert, Eliseo
date: 2020-11-13
extension: .txt
mime: text/plain
words: 980
sentence: 41
flesch: 53
cache: cache/cord-288425-po35m6d9.txt
txt: txt/cord-288425-po35m6d9.txt
title:
  Field evaluation of a rapid antigen test (Panbio™ COVID-19 Ag Rapid Test Device) for COVID-19 diagnosis in primary healthcare centers

summary:
  We would also like to thank María José Beltrán, Pilar Botija and Ana Sanmartín for 180 assistance in organizing RAD testing in primary healthcare centers. Presence of SARS-CoV-2 in cell cultures was confirmed by RT-PCR.


id: cord-254278-awdqguoo
author: Khan, Suliman
title: Association of COVID-19 infection with pregnancy outcomes in healthcare workers and general women
date: 2020-04-08
extension: .txt
mime: text/plain
words: 776
sentence: 34
flesch: 59
cache: cache/cord-254278-awdqguoo.txt
txt: txt/cord-254278-awdqguoo.txt
summary:
  Based on our findings in these seventeen patients, we suggest that COVID-19 infection 12 may lead to the occurrence of neonatal pneumonia and preterm delivery. However, we cannot In summary, we found two neonates suspected for COVID-19 infection and five neonates 1 with neonatal pneumonia, suggesting the possibility that adverse pregnancy outcomes may be 2 linked to COVID-19 infection.


id: cord-030061-55ntc4wj
author: Helleberg, Marie
title: Invasive aspergillosis in patients with severe COVID-19 pneumonia
date: 2020-08-05
extension: .txt
mime: text/plain
words: 612
sentence: 22
flesch: 27
cache: cache/cord-030061-55ntc4wj.txt
txt: txt/cord-030061-55ntc4wj.txt
summary:
  key: cord-030061-55ntc4wj authors: Helleberg, Marie; Steensen, Morten; Arendrup, Maiken Cavling title: Invasive aspergillosis in patients with severe COVID-19 pneumonia date: 2020-08-05 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.07.047 sha: doc_id: 30061 cord_uid: 55ntc4wj nan intensive care units (ICUs) due to respiratory failure. 1 Other severe viral pneumonias may also increase the risk of invasive aspergillosis 14 significantly.


id: cord-032016-2rzszcke
author: Kumar, Anil
title: Sarcoidosis, Steroids and Strongyloides -What’s the Catch?()
date: 2020-09-17
extension: .txt
mime: text/plain
words: 552
sentence: 28
flesch: 32
cache: cache/cord-032016-2rzszcke.txt
txt: txt/cord-032016-2rzszcke.txt
summary:
  Chronic gastrointestinal infection with S. stercoralis can have either no symptoms or mild nonspecific gastrointestinal, respiratory, and cutaneous symptoms. It is important for clinicians to rule out gastrointestinal infection with S. stercoralis in patients on long term steroids in order to prevent hyperinfection syndrome.


id: cord-269345-5tlyy8jp
author: Minuz, Pietro
title: High rate of pulmonary thromboembolism in patients with SARS-CoV-2 pneumonia
date: 2020-06-18
extension: .txt
mime: text/plain
words: 693
sentence: 24
flesch: 41
cache: cache/cord-269345-5tlyy8jp.txt
txt: txt/cord-269345-5tlyy8jp.txt
summary:
  84 Considering that an undiagnosed thromboembolic process might worsen patients´ outcome, we 86 would suggest including a CTPA scan in the diagnostic assessment of patients with Sars-CoV-2 87 pneumonia, high D-dimer, and refractory or rapidly deteriorating hypoxemic respiratory failure. Although the prevalence in our small cohort of 72 non-ICU patients is less than the one recently reported in ICU patients [1] , it seems to confirm the 73 increased risk of PTE in COVID-19 patients.


id: cord-257696-ybu772zw
author: Bartoletti, Michele
date: 2020-09-22
extension: .txt
mime: text/plain
words: 921
sentence: 43
flesch: 38
cache: cache/cord-257696-ybu772zw.txt
txt: txt/cord-257696-ybu772zw.txt
title:
  Efficacy of corticosteroid treatment for hospitalized patients with severe COVID-19: a multicenter study

summary:
  key: cord-257696-ybu772zw authors: Bartoletti, Michele; Marconi, Lorenzo; Scudeller, Luigia; Pancaldi, Livia; Tedeschi, Sara; Giannella, Maddalena; Rinaldi, Matteo; Bussini, Linda; Valentini, Ilaria; Ferravante, Anna Filomena; Potalivo, Antonella; Marchionni, Elisa; Fornaro, Giacomo; Pascale, Renato; Pasquini, Zeno; Puoti, Massimo; Merli, Marco; Barchiesi, Francesco; Volpato, Francesca; Rubin, Arianna; Saracino, Annalisa; Tonetti, Tommaso; Gaibani, Paolo; Ranieri, Vito Marco; Viale, Pierluigi; Cristini, Francesco title: Efficacy of corticosteroid treatment for hospitalized patients with severe COVID-19: a multicenter study date: 2020-09-22 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.014 sha: doc_id: 257696 cord_uid: ybu772zw OBJECTIVES: In this study we were not able to find a lower mortality rate among hospitalized patients Characteristics of and Important Lessons From the Coronavirus 333 Disease 2019 (COVID-19) Outbreak in China Characteristics, Comorbidities, and Outcomes Among 5700 Patients Hospitalized With Critical Care Utilization for the COVID-19 Outbreak in Early Experience and Forecast During an Emergency Response Clinical features of patients infected with 2019 novel 346 coronavirus in Wuhan Development and validation of 351 a prediction model for severe respiratory failure in hospitalized patients with SARS-Cov-2 infection: 352 a multicenter cohort study (PREDI-CO study), Clinical microbiology and infection : the official Tocilizumab in patients with severe COVID-19: a retrospective 362 cohort study Impact of corticosteroid therapy 364 on outcomes of persons with SARS-CoV-2, SARS-CoV, or MERS-CoV infection: a systematic 365 review and meta-analysis Dexamethasone in Hospitalized Patients with Covid-19 -Preliminary Methylprednisolone as Adjunctive Therapy for Patients Hospitalized With COVID-19 (Metcovid): A Placebo-Controlled Trial


id: cord-275556-798oed8n
author: Piubelli, Chiara
date: 2020-10-12
extension: .txt
mime: text/plain
words: 611
sentence: 23
flesch: 45
cache: cache/cord-275556-798oed8n.txt
txt: txt/cord-275556-798oed8n.txt
title:
  Overall decrease of SARS-CoV-2 viral load and reduction of clinical burden: the experience of a Northern Italy hospital

summary:
  In this work, we aimed at evaluating a possible association between the severity of clinical manifestations and viral load over time, during the epidemiological transition from high to low transmission setting. As for viral load, we observed a trend of Ct increasing from a median value of 24 (IQR 19-29) to 34 (IQR 29-37) between March and May, with a statistically significant difference between March and April (Pairwise Wilcoxon test with Stepdown Bonferroni Adjustment for multiple testing, p=0.0003).


id: cord-256402-b5fel2d3
author: Gevers, S.
title: Safety considerations of chloroquine and hydroxychloroquine in treatment of COVID-19
date: 2020-05-16
extension: .txt
mime: text/plain
words: 887
sentence: 39
flesch: 42
cache: cache/cord-256402-b5fel2d3.txt
txt: txt/cord-256402-b5fel2d3.txt
summary:
  Psychiatric side effects include sleeplessness, agitation, psychosis, depression, anxiety, aggressiveness and confusion; with psychiatric side effects starting within a few days after beginning of treatment and improving after cessation of treatment. Reported cardiac side effects of CQ/HCQ include conduction disturbances (bundle-branch block, incomplete or complete atrioventricular block, QT-prolongation and subsequent torsade de pointes) and cardiomyopathy (hypertrophy and congestive heart failure).


id: cord-253250-zet48zcl
author: Thaden, J.T.
date: 2020-09-09
extension: .txt
mime: text/plain
words: 875
sentence: 24
flesch: 18
cache: cache/cord-253250-zet48zcl.txt
txt: txt/cord-253250-zet48zcl.txt
title:
  When two for the price of one isn’t a bargain: Estimating prevalence and microbiology of bacterial co-infections in patients with COVID-19

summary:
  There was heterogeneity in the outcomes of the studies that were included in the meta-analysis, as some reported whether bacterial infection was noted on presentation to the hospital (n=20 studies; termed bacterial co-infection), while the remaining studies reported whether a concomitant bacterial infection developed during the course of the patient's hospitalization (n=8 studies; termed secondary bacterial infection). Interestingly, stratification of patients by illness severity showed that bacterial infections were more prevalent in fatal (11.6%) and ICU (8.1%) cases relative to non-ICU hospitalized patients (5.8%).


id: cord-009295-4c0zwhdh
author: Bal, A.
date: 2020-03-28
extension: .txt
mime: text/plain
words: 1254
sentence: 52
flesch: 49
cache: cache/cord-009295-4c0zwhdh.txt
txt: txt/cord-009295-4c0zwhdh.txt
title:
  Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del)

summary:
  A novel coronavirus from patients with pneumonia in China First cases of coronavirus disease 2019 (COVID-19) in the WHO European region Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow Amino acid analysis for the SARS-CoV-2 outbreak Letter to the Editor / Clinical Microbiology and Infection xxx (xxxx) A mean of 19 445 767 reads per sample were generated, of which a mean of 605 243 reads per sample were mapped to the SARS-CoV-2 reference genome.


id: cord-009675-utz0iazs
author: Madeley, C. R.
title: Are point‐of‐care (POC) virological tests what is needed?
date: 2007-06-05
extension: .txt
mime: text/plain
words: 1264
sentence: 55
flesch: 48
cache: cache/cord-009675-utz0iazs.txt
txt: txt/cord-009675-utz0iazs.txt
summary:
  Each of these components needs to be carefully addressed when using POC tests for the diagnosis of respiratory tract infections. Given the enthusiasm with which POC tests are being developed, it is likely that they will be used more and more widely.


id: cord-314288-6vh7dvad
author: Leibovici, L.
title: Submissions and publications in Corona times
date: 2020-05-15
extension: .txt
mime: text/plain
words: 1094
sentence: 50
flesch: 52
cache: cache/cord-314288-6vh7dvad.txt
txt: txt/cord-314288-6vh7dvad.txt
summary:
  Observational studies: Now we have a good idea from published studies on the clinical course of COVID-19, and further descriptions of small groups of patients have little to add. However systematic reviews of observational studies, and especially meta-analyses of such studies assessing the efficiency of drugs, are problematic.


id: cord-298441-77w86l8q
author: Lombardi, Andrea
date: 2020-06-20
extension: .txt
mime: text/plain
words: 1439
sentence: 52
flesch: 46
cache: cache/cord-298441-77w86l8q.txt
txt: txt/cord-298441-77w86l8q.txt
title:
  Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy

summary:
  To answer this question, we reviewed all the 59 nasopharyngeal swab performed in HCWs exposed to confirmed cases of COVID-19 at the 60 Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico located in Milan, the capital 61 of Lombardy, by large the Italian region mostly affected by We assessed 62 frequency of positive tests among symptomatic and asymptomatic HCWs and evaluated the 63 association between occupation, symptoms (type and number), and presence of the infection. The median time from first positive test to a negative test was 27 days (95% CI: 24-30).


id: cord-286525-0354438s
author: Lee, Todd C.
title: Tocilizumab versus the covid19 tempest: all’s well that ends well or much ado about nothing?
date: 2020-09-29
extension: .txt
mime: text/plain
words: 1440
sentence: 53
flesch: 35
cache: cache/cord-286525-0354438s.txt
txt: txt/cord-286525-0354438s.txt
summary:
  As such, the tocilizumab group was further along in the illness trajectory with a median of One of the unexpected findings from this study was an observed lack of benefit from steroids in contrast to the RECOVERY randomized controlled trial results [4] or a recent meta-analysis of steroid trials in critically ill patients. The phase III COVACTA trial (NCT04317092) found tocilizumab did not reduce mortality in hospitalized patients with severe COVID-19 pneumonia


id: cord-297470-lx3xwg92
author: Pan, Yunbao
date: 2020-10-07
extension: .txt
mime: text/plain
words: 1602
sentence: 66
flesch: 43
cache: cache/cord-297470-lx3xwg92.txt
txt: txt/cord-297470-lx3xwg92.txt
title:
  Seroprevalence of SARS-CoV-2 immunoglobulin antibodies in Wuhan, China: part of the city-wide massive testing campaign

summary:
  Most of Wuhan residents are still susceptible to this virus. A recent study detected 17,368 individuals from different geographic regions in China, including 1993 residents from different Wuhan sub-cohorts.


id: cord-327253-gge6wzly
author: Villa, Simone
title: Stigma at the time of the COVID-19 pandemic
date: 2020-08-07
extension: .txt
mime: text/plain
words: 1376
sentence: 62
flesch: 47
cache: cache/cord-327253-gge6wzly.txt
txt: txt/cord-327253-gge6wzly.txt
summary:
  In Italy, some politicians accused Chinese people of poor hygiene and unhealthy cultural practices, including that of eating live mice. The Guardian Asian Americans report over 650 racist acts over last week, new data says Politician apologizes for saying coronavirus caused by Chinese people eating 'live mice' Italiani untori You Could Lick the Benches': Life for the First Wave of U Immunity passports in the context of COVID-19.


id: cord-291729-4l4v9jxd
author: de Salazar, Adolfo
title: Sample pooling for SARS-COV-2 RT-PCR screening
date: 2020-09-10
extension: .txt
mime: text/plain
words: 2642
sentence: 90
flesch: 42
cache: cache/cord-291729-4l4v9jxd.txt
txt: txt/cord-291729-4l4v9jxd.txt
summary:
  SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Viral load of SARS-CoV-2 in clinical samples The Detection of Defective Members of Large Populations Improved matrix pooling A methodology for deriving the sensitivity of pooled testing, based on viral load progression and pooling dilution Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR COVID-19 diagnosis and management: a comprehensive review Screening tests: Can we get more by doing less Pooling Strategies to Reduce the Cost of HIV-1 RNA Load Monitoring in a Resource-Limited Setting Pooled Nucleic Acid Testing to Detect Antiretroviral Treatment Failure in Mexico Occult HBV infection in HIV-infected adults and evaluation of pooled NAT for HBV Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources Pooled-sample analysis strategies for COVID-19 mass testing: a simulation study Sample Pooling as a Strategy to Detect Community Transmission of SARS-CoV-2 Evaluation of COVID-19 RT-qPCR test in multi-sample pools Pooling of nasopharyngeal swab specimens for SARS-CoV-2 detection by RT-PCR Evaluating the efficiency of specimen pooling for PCR-based detection of COVID-19 Pooling of samples for testing for SARS-CoV-2 in asymptomatic people False Negative Tests for SARS-CoV-2 Infection -Challenges and Implications Predicting infectious SARS-CoV-2 from diagnostic samples Optimization of group size in pool testing strategy for SARS-CoV-2: A simple mathematical model Simulation of Pool Testing to Identify Patients With Coronavirus Disease 2019 key: cord-291729-4l4v9jxd authors: de Salazar, Adolfo; Aguilera, Antonio; Trastoy, Rocio; Fuentes, Ana; Alados, Juan Carlos; Causse, Manuel; Galán, Juan Carlos; Moreno, Antonio; Trigo, Matilde; Pérez-Ruiz, Mercedes; Roldán, Carolina; José Pena, Ma; Bernal, Samuel; Serrano-Conde, Esther; Barbeito, Gema; Torres, Eva; Riazzo, Cristina; Cortes-Cuevas, Jose Luis; Chueca, Natalia; Coira, Amparo; Sanchez-Calvo, Juan M.; Marfil, Eduardo; Becerra, Federico; Gude, María José; Pallarés, Ángeles; Pérez Del Molino, María Luisa; García, Federico title: Sample pooling for SARS-COV-2 RT-PCR screening date: 2020-09-10 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.008 sha: doc_id: 291729 cord_uid: 4l4v9jxd OBJECTIVE: To evaluate the efficacy of sample pooling compared to the individual analysis for the diagnosis of COVID-19, by using different commercial platforms for nucleic acid extraction and amplification.


id: cord-334835-j6u8t8j2
author: Berenguer, Juan
date: 2020-08-04
extension: .txt
mime: text/plain
words: 1740
sentence: 79
flesch: 48
cache: cache/cord-334835-j6u8t8j2.txt
txt: txt/cord-334835-j6u8t8j2.txt
title:
  Characteristics and predictors of death among 4,035 consecutively hospitalized patients with COVID-19 in Spain

summary:
  Recent studies with COVID-19 patients indicate that 252 younger hospitalized individuals were more likely to be obese (23) and that obesity is associated 253 with severe pictures (23-25) and increased mortality (14). We aimed to analyse the characteristics and predictors of death in hospitalized patients with COVID-19 in Spain.


id: cord-283411-40ojqv1y
author: Ben-Shmuel, Amir
date: 2020-09-10
extension: .txt
mime: text/plain
words: 1176
sentence: 51
flesch: 46
cache: cache/cord-283411-40ojqv1y.txt
txt: txt/cord-283411-40ojqv1y.txt
title:
  Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities

summary:
  283 International journal of infectious diseases : IJID : official publication of the International Society for 284 Infectious Diseases Detection of airborne severe 286 acute respiratory syndrome (SARS) coronavirus and environmental contamination in SARS outbreak 287 units. In this study, viral RNA contamination was found in 46% of the surface and air samples.


id: cord-292296-nocmabcg
author: Shang, L.
title: Fangcang shelter hospitals in COVID-19 pandemic: the practice and its significance
date: 2020-05-01
extension: .txt
mime: text/plain
words: 1576
sentence: 63
flesch: 41
cache: cache/cord-292296-nocmabcg.txt
txt: txt/cord-292296-nocmabcg.txt
summary:
  In this issue of Clinical Microbiology and Infection, Wang et al. described the work flow of Fangcang shelter hospitals and reported the clinical characteristics of COVID-19 patients in Dongxihu Fangcang shelter hospital, one of the largest Fangcang shelter hospitals in Wuhan [9] . key: cord-292296-nocmabcg authors: Shang, L.; Xu, J.; Cao, B. title: Fangcang shelter hospitals in COVID-19 pandemic: the practice and its significance date: 2020-05-01 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.04.038 sha: doc_id: 292296 cord_uid: nocmabcg nan Coronavirus disease 2019 (COVID-19), an emerging respiratory infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been spreading across the world rapidly and claiming tens of thousands of lives.


id: cord-265363-xw56intn
author: Gautret, P.
date: 2014-12-12
extension: .txt
mime: text/plain
words: 3115
sentence: 136
flesch: 42
cache: cache/cord-265363-xw56intn.txt
txt: txt/cord-265363-xw56intn.txt
title:
  Incidence of Hajj-associated febrile cough episodes among French pilgrims: a prospective cohort study on the influence of statin use and risk factors

summary:
  [15] , suggest that Hajj travellers departing from Marseille represent a category of travellers particularly at risk for travel-related diseases and that their socio-economic conditions should be considered during the pre-travel visit regarding cost-effective vaccines. Cough was defined as occurrence of cough with or without sputum in an individual without chronic cough and subjective aggravation of cough in individuals suffering from chronic respiratory diseases.


id: cord-010162-hfo35gsq
author: Saikku, Pekka
title: Atypical respiratory pathogens
date: 2014-12-29
extension: .txt
mime: text/plain
words: 3071
sentence: 133
flesch: 32
cache: cache/cord-010162-hfo35gsq.txt
txt: txt/cord-010162-hfo35gsq.txt
summary:
  According to seroepidemiologic surveys, Chlamydia pneumoniae infections are 20-50 times more common than Chlamydia psitfari infections [15,16]. It should also be attempted in Chlamydia pneumoniae infections in order to obtain information on disease associations and strain variability of this newly recognized pathogen.


id: cord-314808-ssiggi2z
author: Pappas, G.
title: Psychosocial consequences of infectious diseases
date: 2014-12-12
extension: .txt
mime: text/plain
words: 3183
sentence: 110
flesch: 38
cache: cache/cord-314808-ssiggi2z.txt
txt: txt/cord-314808-ssiggi2z.txt
summary:
  An infectious diseases specialist is on a plane, returning from an international congress on infectious diseases; several hours earlier, he attended a lecture about the then evolving severe acute respiratory syndrome (SARS) outbreak. These three individuals, among many others, experience levels of fear associated with infectious diseases in their everyday lives.


id: cord-257248-aii0tj9x
author: O'Grady, K.F.
date: 2016-02-22
extension: .txt
mime: text/plain
words: 3365
sentence: 117
flesch: 35
cache: cache/cord-257248-aii0tj9x.txt
txt: txt/cord-257248-aii0tj9x.txt
title:
  Prevalence, codetection and seasonal distribution of upper airway viruses and bacteria in children with acute respiratory illnesses with cough as a symptom

summary:
  Bacterial colonization dampens influenza-mediated acute lung injury via induction of M2 alveolar macrophages Association between respiratory infections in early life and later asthma is independent of virus type The development of chronic cough in children following presentation to a tertiary paediatric emergency department with acute respiratory illness: study protocol for a prospective cohort study Successful application of a simple specimen transport method for the conduct of respiratory virus surveillance in remote Indigenous communities in Australia Mailed versus frozen transport of nasal swabs for surveillance of respiratory bacteria in remote Indigenous communities in Australia Aetiological role of common respiratory viruses in acute lower respiratory infections in children under five years: a systematic review and meta-analysis The co-pathogenesis of influenza viruses with bacteria in the lung Non-typeable Haemophilus influenzae, an under-recognised pathogen Airway microbiota and acute respiratory infection in children Nasopharyngeal microbiota in healthy children and pneumonia patients Viruses and bacteria in sputum samples of children with community-acquired pneumonia Acute respiratory infection in children from developing nations: a multi-level study. Viral bacterial co-infection of the respiratory tract during early childhood Cough formation in viral infections in children Is virus coinfection a predictor of severity in children with viral respiratory infections? Staphylococcus aureus colonization is associated with wheeze and asthma among US children and young adults A prospective study of agents associated with acute respiratory infection among young American Indian children Three-weekly doses of azithromycin for indigenous infants hospitalized with bronchiolitis: a multicentre, randomized, placebo-controlled trial Upper airway viruses and bacteria detection in clinical pneumonia in a population with high nasal colonisation do not relate to clinical signs Epidemiology and etiology of childhood pneumonia in 2010: estimates of incidence, severe morbidity, mortality, underlying risk factors and causative pathogens for 192 countries Evidence for a causal relationship between respiratory syncytial virus infection and asthma Does the microbiota regulate immune responses outside the gut?


id: cord-270947-6e5cw2q9
author: Huang, H.-S.
date: 2017-12-05
extension: .txt
mime: text/plain
words: 4034
sentence: 158
flesch: 32
cache: cache/cord-270947-6e5cw2q9.txt
txt: txt/cord-270947-6e5cw2q9.txt
title:
  Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis

summary:
  Estimates of world-wide distribution of child deaths from acute respiratory infections Prevalence and correlation of infectious agents in hospitalized children with acute respiratory tract infections in Central China Community-acquired pneumonia requiring hospitalization: 5-year prospective study The effect of rapid respiratory viral diagnostic testing on antibiotic use in a children's hospital Cost-effective use of rapid diagnostic techniques in the treatment and prevention of viral respiratory infections Excessive antibiotic use for acute respiratory infections in the United States Detection of respiratory viruses by molecular methods Current approaches for diagnosis of influenza virus infections in humans Current best practices for respiratory virus testing Cost-effectiveness of rapid diagnosis of viral respiratory tract infections in pediatric patients Cost analysis of multiplex PCR testing for diagnosing respiratory virus infections Thermally multiplexed polymerase chain reaction Genotyping of respiratory syncytial virus (RSV) group A in Stockholm, Sweden, using PCR and two-dimensional melting curve analysis Nucleic acid amplificationebased diagnosis of respiratory virus infections Evaluation of multiple test methods for the detection of the novel 2009 influenza A (H1N1) during the New York City outbreak Emerging molecular assays for detection and characterization of respiratory viruses Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay Evaluation of a multiplexed PCR assay for detection of respiratory viral pathogens in a public health laboratory setting RespiFinder: a new multiparameter test to differentially identify fifteen respiratory viruses Respiratory viruses in children admitted to hospital intensive care units: evaluating the CLART® Pneumovir DNA array Broad respiratory virus detection in infants hospitalized for bronchiolitis by use of a multiplex RT-PCR DNA microarray system Simultaneous detection and high-throughput identification of a panel of RNA viruses causing respiratory tract infections Rapid detection of respiratory tract viral infections and coinfections in patients with influenza-like illnesses by use of reverse transcriptionePCR DNA microarray systems The FilmArray® respiratory panel: an automated, broadly multiplexed molecular test for the rapid and accurate detection of respiratory pathogens Comparison of the FilmArray RP, Verigene RVþ, and Prodesse ProFLUþ/FASTþ multiplex platforms for detection of influenza viruses in clinical samples from the 2011e2012 influenza season in Belgium The PRISMA statement for reporting systematic reviews and meta-analyses of studies that evaluate healthcare interventions: explanation and elaboration Cochrane Diagnostic Test Accuracy Working Group. key: cord-270947-6e5cw2q9 authors: Huang, H.-S.; Tsai, C.-L.; Chang, J.; Hsu, T.-C.; Lin, S.; Lee, C.-C. title: Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis date: 2017-12-05 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2017.11.018 sha: doc_id: 270947 cord_uid: 6e5cw2q9 OBJECTIVES:


id: cord-279111-jaa45kyc
author: Ieven, M.
date: 2018-02-12
extension: .txt
mime: text/plain
words: 4083
sentence: 162
flesch: 41
cache: cache/cord-279111-jaa45kyc.txt
txt: txt/cord-279111-jaa45kyc.txt
title:
  Aetiology of lower respiratory tract infection in adults in primary care: a prospective study in 11 European countries

summary:
  Influenza virus, human parainfluenza viruses and human respiratory syncytial virus as well as human rhinovirus, human coronavirus and human metapneumovirus were detected significantly more frequently in LRTI patients than in controls. Influenza virus, human parainfluenza viruses and human respiratory syncytial virus as well as human rhinovirus, human coronavirus and human metapneumovirus were detected significantly more frequently in LRTI patients than in controls.


id: cord-256429-ntx0eay0
author: Hao, W.
title: First atypical case of 2019 novel coronavirus in Yan'an, China
date: 2020-02-20
extension: .txt
mime: text/plain
words: 499
sentence: 24
flesch: 60
cache: cache/cord-256429-ntx0eay0.txt
txt: txt/cord-256429-ntx0eay0.txt
summary:
  Moreover, the rapid progression of chest imaging in the short term (<7 days) has critical diagnostic value for patients with negative 2019-nCoV nucleic acid tests. Clinical features of patients infected with 2019 novel coronavirus in Wuhan A novel coronavirus from patients with pneumonia in China Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia W-DH and X-QH obtained and analysed the clinical data and produced the figure.


id: cord-031493-w8agvg9g
author: Davido, Benjamin
title: Possible therapies of Post-COVID-19 chronic symptoms()
date: 2020-09-06
extension: .txt
mime: text/plain
words: 154
sentence: 4
flesch: 29
cache: cache/cord-031493-w8agvg9g.txt
txt: txt/cord-031493-w8agvg9g.txt
summary:
  key: cord-031493-w8agvg9g authors: Davido, Benjamin; Seang, Sophie; Barizien, Nicolas; Tubiana, Roland; de Truchis, Pierre title: Possible therapies of Post-COVID-19 chronic symptoms() date: 2020-09-06 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.001 sha: doc_id: 31493 cord_uid: w8agvg9g nan responsible for dysautonomia in patients with persistent symptoms following acute SARS-23 COV2 infection. Actually, we did not state that these symptoms of autonomic impairment do not require 28 specific treatment, but we believe it must be a case by case management depending on the breathing/hyperventilation syndrome in adults Efficacy of 68 Therapies for Postural Tachycardia Syndrome: A Systematic Review and Meta-69 analysis


id: cord-344027-qghktrm1
author: Fiolet, Thibault
date: 2020-10-17
extension: .txt
mime: text/plain
words: 330
sentence: 10
flesch: 23
cache: cache/cord-344027-qghktrm1.txt
txt: txt/cord-344027-qghktrm1.txt
title:
  'Effect of hydroxychloroquine with or without azithromycin on the mortality of COVID-19 patients' – Author’s reply

summary:
  key: cord-344027-qghktrm1 authors: Fiolet, Thibault; Guihur, Anthony; Rebeaud, Mathieu E.; Mulot, Matthieu; Peiffer-Smadja, Nathan; Mahamat-Saleh, Yahya title: 'Effect of hydroxychloroquine with or without azithromycin on the mortality of COVID-19 patients' – Author’s reply date: 2020-10-17 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.10.002 sha: doc_id: 344027 cord_uid: qghktrm1 nan 3) A critical analysis of chloroquine and hydroxychloroquine 178 clinical pharmacology Concentration-dependent mortality of chloroquine in overdose Utilization 184 of COVID-19 treatments and clinical outcomes among patients with cancer: A COVID-185 19 and Cancer Consortium (CCC19) cohort study Interventions 188 for treatment of COVID-19: A living systematic review with meta-analyses and trial 189 sequential analyses (The LIVING Project) Mortality outcomes with hydroxychloroquine and chloroquine in COVID-19: an 193 international collaborative meta-analysis of randomized trials Hydroxychloroquine as pre-exposure prophylaxis for COVID-19 in healthcare workers: 203 a randomized trial


id: cord-295479-mcfqs7vf
author: Davido, Benjamin
title: Post-COVID-19 chronic symptoms: a post-infectious entity?()
date: 2020-07-23
extension: .txt
mime: text/plain
words: 196
sentence: 4
flesch: 9
cache: cache/cord-295479-mcfqs7vf.txt
txt: txt/cord-295479-mcfqs7vf.txt
summary:
  The ALBACOVID registry Cerebrovascular disease in patients with COVID-19: 106 neuroimaging, histological and clinical description Kawasaki-like multisystem inflammatory syndrome in children during the covid-19 Chikungunya-Induced Arthritis in Reunion Island: A 113 Long-Term Observational Follow-Up Study Showing Frequently Persistent Joint 114 Some Cases of Persistent Chikungunya Immunoglobulin M Positivity, and 115 Surprisingly today, while we are fearing a second wave, we receive more and more of those COVID-19 : point épidémiologique du 21 mai Assistance Publique-Hôpitaux de Paris' response to the COVID-19 88 pandemic Anosmia and Ageusia: Common Findings 90 in COVID-19 Patients Patients Recovered from COVID-19 Active Epstein-Barr virus infection in 95 post-viral fatigue syndrome serological IgG antibody response on the Abbott Architect for established SARS-CoV-99 2 infection Neurologic manifestations in hospitalized patients 102 with COVID-19:


id: cord-325186-nq6ay4eo
author: Sieswerda, Elske
title: Recommendations for antibacterial therapy in adults with COVID-19 – An evidence based guideline
date: 2020-10-01
extension: .txt
mime: text/plain
words: 857
sentence: 36
flesch: 26
cache: cache/cord-325186-nq6ay4eo.txt
txt: txt/cord-325186-nq6ay4eo.txt
summary:
  BY THE GUIDELINE AND RECOMMENDATIONS: We assessed evidence on the risk of bacterial infections in hospitalized COVID-19 patients, the associated bacterial pathogens, how to diagnose bacterial infections and how to treat bacterial infections. Although the evidence base on bacterial infections in COVID-19 is currently limited, available evidence supports restrictive antibiotic use from an antibiotic stewardship perspective, especially upon admission.


id: cord-328499-d6cvaxm9
author: Matzkies, Lucie-Marie
title: Lack of sensitivity of an IVD/CE-labeled kit targeting the S gene for detection of SARS-CoV-2
date: 2020-07-08
extension: .txt
mime: text/plain
words: 572
sentence: 24
flesch: 50
cache: cache/cord-328499-d6cvaxm9.txt
txt: txt/cord-328499-d6cvaxm9.txt
summary:
  Clinical samples (n=101) obtained from patients with symptoms compatible to COVID-19 were studied. When using the VIASURE test for routine testing, a significant number of COVID-19 positive samples would have been missed.


id: cord-294392-a8s66g96
author: Zhang, Shuai
date: 2020-09-07
extension: .txt
mime: text/plain
words: 986
sentence: 44
flesch: 39
cache: cache/cord-294392-a8s66g96.txt
txt: txt/cord-294392-a8s66g96.txt
title:
  Factors associated with asymptomatic infection in health-care workers with SARS-CoV-2 infection in Wuhan, China: a multi-center retrospective cohort study

summary:
  No significant differences were seen in any 164 high-risk procedures between asymptomatic HCWs and symptomatic HCWs. Compared with 165 symptomatic HCWs, asymptomatic HCWs more consistently used hand washing, isolation gown, eye 166 protection, N95 respirators, gloves, and hair cover for protection (P<0.001).


id: cord-264261-98h1bmb2
author: Caruana, Giorgia
title: Diagnostic strategies for SARS-CoV-2 infection and interpretation of microbiological results
date: 2020-06-25
extension: .txt
mime: text/plain
words: 1419
sentence: 47
flesch: 32
cache: cache/cord-264261-98h1bmb2.txt
txt: txt/cord-264261-98h1bmb2.txt
summary:
  WHO guidelines for 396 the global surveillance of severe acute respiratory syndrome (SARS): updated 397 recommendations Serological assays for emerging 401 coronaviruses: challenges and pitfalls Novel antibody epitopes dominate the antigenicity of spike 403 glycoprotein in SARS-CoV-2 compared to SARS-CoV Potent binding of 2019 novel coronavirus spike protein by a SARS 407 coronavirus-specific human monoclonal antibody Lateral flow assays SARS-CoV-2 viral load in 413 upper respiratory specimens of infected patients Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 China: a report of 1014 cases Fecal specimen diagnosis 2019 Samples like blood and urines were found to be weakly-to-none sensitive, while the virus was 231 also found in feces and perineal swabs of patients with gastro-intestinal symptoms [44] [45] , Improved molecular diagnosis of COVID-19 by the novel, highly sensitive 316 and specific COVID-19-RdRp/Hel real-time reverse transcription-polymerase chain 317 reaction assay validated in vitro and with clinical specimens Ten years of R&D and full automation 320 in molecular diagnosis Letter to the editor: 322 SARS-CoV-2 detection by real-time RT-PCR Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction-Based 330 SARS-CoV-2 Tests by Time Since Exposure Sources of pre-analytical, analytical and post-analytical errors in 332 the microbiology laboratory PCR inhibitors-occurrence, 336 properties and removal SARS-COV-2 diagnostic pipeline Xpert® Xpress SARS-CoV-2 has received FDA 340 Purification and enrichment of 343 virus samples utilizing magnetic beads on a microfluidic system High-speed RNA microextraction technology 346 using magnetic oligo-dT beads and lateral magnetophoresis Parallel RNA extraction 349 using magnetic beads and a droplet array Viral DNA/RNA 96 Kit; c2020 351 EZ1 Advanced XL; c2020 IDEAL96 Automated Extraction Robot; c2020 Multifunctional device for 360 nucleic acid extraction based on magnetic separation and its co-working with liquid 361 handling system for high throughput sample preparation A simple 364 magnetic nanoparticles-based viral RNA extraction method for efficient detection of 365 Profile of specific antibodies to the SARS-associated 369 coronavirus Antibody responses to SARS-CoV-2 in patients of 373 novel coronavirus disease 2019 Longitudinal Monitoring of SARS-CoV-2 IgM and IgG Seropositivity 378 to Detect COVID-19 Antibody 387 responses to SARS-CoV-2 in patients with COVID-19 Kinetics of serologic responses to MERS coronavirus infection in humans, South 392 Korea Antigenic relationships amongst coronaviruses.


id: cord-304710-gjb6zo81
author: Khan, S.
title: Novel coronavirus: how things are in Wuhan
date: 2020-02-11
extension: .txt
mime: text/plain
words: 1372
sentence: 58
flesch: 48
cache: cache/cord-304710-gjb6zo81.txt
txt: txt/cord-304710-gjb6zo81.txt
summary:
  The latest 2019 novel coronavirus outbreak in Wuhan, China Coronavirus claims first life outside China as Wuhan enforces quarantine for all suspected patients China coronavirus: Wuhan medical staff being infected at much faster pace than reported as national death toll hits 26 Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China Wuhan calls for more material help to deal with virus. A total of 15 medical staff have been infected, and one doctor has died from 2019n-CoV infection in Wuhan hospital


id: cord-283818-4m9p717r
author: Yan, Chao
date: 2020-04-08
extension: .txt
mime: text/plain
words: 1600
sentence: 64
flesch: 49
cache: cache/cord-283818-4m9p717r.txt
txt: txt/cord-283818-4m9p717r.txt
title:
  Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay

summary:
  Novel coronavirus (2019-nCoV) situation report-7: 27 293 Genomic characterisation and 295 epidemiology of 2019 novel coronavirus: implications for virus origins and receptor 296 binding The global 298 spread of 2019-nCoV: a molecular evolutionary analysis Divergence of the Novel Coronavirus (2019-nCoV) Originating in China Laboratory readiness and response for novel coronavirus (2019-nCoV) in expert 305 laboratories in 30 EU/EEA countries Loop-mediated isothermal amplification of DNA Rapid and sensitive detection of 311 novel avian-origin influenza A (H7N9) virus by reverse transcription loop-mediated 312 isothermal amplification combined with a lateral-flow device A Rapid and Specific Assay 315 for the Detection of Visual detection of west nile 317 virus using reverse transcription loop-mediated isothermal amplification combined 318 with a vertical flow visualization strip Rapid and specific detection of Asian-and African-lineage Zika 321 viruses Survey and Visual Detection of 323 Zaire ebolavirus in Clinical Samples Targeting the Nucleoprotein Gene in Sierra 324 A real-time 326 reverse transcription loop-mediated isothermal amplification assay for the rapid 327 detection of yellow fever virus Loop-mediated isothermal amplification 329 (LAMP): principle, features, and future prospects Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR Molecular 334 Diagnosis of a Novel Coronavirus (2019-nCoV) key: cord-283818-4m9p717r authors: Yan, Chao; Cui, Jinghua; Huang, Lei; Du, Bing; Chen, Lu; Xue, Guanhua; Li, Shaoli; Zhang, Weiwei; Zhao, Linqing; Sun, Yu; Yao, Hailan; Li, Nannan; Zhao, Hanqing; Feng, Yanling; Liu, Shiyu; Zhang, Qun; Liu, Di; Yuan, Jing title: Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay date: 2020-04-08 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.04.001 sha: doc_id: 283818 cord_uid: 4m9p717r OBJECTIVE: To evaluate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of SARS-CoV-2, and compare it with RT polymerase chain reaction (RT-PCR).


id: cord-279125-w6sh7xpn
author: Egli, Adrian
title: Digital microbiology
date: 2020-06-27
extension: .txt
mime: text/plain
words: 1603
sentence: 75
flesch: 34
cache: cache/cord-279125-w6sh7xpn.txt
txt: txt/cord-279125-w6sh7xpn.txt
summary:
  Challenges of digitalisation in the microbiology diagnostic process The collection, quality control and cleaning, storage, security and protection, stewardship and governance, interoperability and interconnection, reporting and visualization, versioning, and sharing 20 of data pose considerable challenges for big data in microbiology diagnostic laboratories. Stud Health Technol MIMIC-III, a freely accessible critical care database The eICU Collaborative Research Database, a freely available multi-center 14 database for critical care research PulseNet and the Changing Paradigm of Laboratory-Based Surveillance Microreact: visualizing and sharing data for genomic epidemiology and 19 phylogeography Nextstrain: real-time tracking of pathogen evolution Improving the quality and workflow of bacterial genome sequencing and 23 analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance 24 platform A comprehensive collection of systems biology data characterizing Infectious Diseases and Associated Ethical Impacts Big data and machine learning in 35 critical care: Opportunities for collaborative research Privacy in the age of medical big data The COMPARE Data Hubs.


id: cord-307273-pplky6g4
author: Schrooyen, Loïc
title: Homeless people hospitalized with COVID-19 in Brussels
date: 2020-08-07
extension: .txt
mime: text/plain
words: 1008
sentence: 44
flesch: 38
cache: cache/cord-307273-pplky6g4.txt
txt: txt/cord-307273-pplky6g4.txt
summary:
  We assessed the prevalence, incidence and outcome of homeless patients hospitalized in our institution with COVID-19 between 3 rd March and 26 th May 2020. Homeless patients were retrospectively identified based on systematic social inquiry performed upon admission.


id: cord-317918-pl625ela
author: Ripa, Marco
title: Secondary Infections in Patients Hospitalized with COVID-19: Incidence and Predictive Factors
date: 2020-10-24
extension: .txt
mime: text/plain
words: 910
sentence: 35
flesch: 34
cache: cache/cord-317918-pl625ela.txt
txt: txt/cord-317918-pl625ela.txt
summary:
  Aim of our study was to describe the incidence and predictive factors of secondary infections in patients with COVID-19. Patients hospitalized with COVID-19 had a high incidence of secondary infections.


id: cord-306083-juysx6yo
author: Choe, Young June
date: 2020-09-10
extension: .txt
mime: text/plain
words: 1750
sentence: 77
flesch: 37
cache: cache/cord-306083-juysx6yo.txt
txt: txt/cord-306083-juysx6yo.txt
title:
  Co-seasonality and co-detection of respiratory viruses and bacteraemia in children: a retrospective analysis

summary:
  Effect of use of 13-valent pneumococcal conjugate vaccine in children on invasive pneumococcal disease in children and adults in the USA: analysis of multisite, populationbased surveillance Global epidemiology of non-influenza RNA respiratory viruses: data gaps and a growing need for surveillance Seasonal invasive pneumococcal disease in children: role of preceding respiratory viral infection Patterns of shedding of myxoviruses and paramyxoviruses in children Incubation periods of acute respiratory viral infections: a systematic review STL: a seasonal-trend decomposition procedure based on loess Seasonality of infectious diseases Influenza virus infection and the risk of serious bacterial infections in young febrile infants Clinical characteristics of children and adults hospitalized for influenza virus infection Prevalence of serious bacterial infections in febrile infants with respiratory syncytial virus infection Bacteraemia and antibiotic use in respiratory syncytial virus infections Secondary bacteremia following adenovirus infection Modulation of Host Immunity by the Human Metapneumovirus key: cord-306083-juysx6yo authors: Choe, Young June; Park, Sangshin; Michelow, Ian C. title: Co-seasonality and co-detection of respiratory viruses and bacteraemia in children: a retrospective analysis date: 2020-09-10 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.09.006 sha: doc_id: 306083 cord_uid: juysx6yo OBJECTIVES:


id: cord-343090-dsjq98ks
author: Fragkou, Paraskevi C.
title: Review of trials currently testing treatment and prevention of COVID-19
date: 2020-05-23
extension: .txt
mime: text/plain
words: 2032
sentence: 87
flesch: 36
cache: cache/cord-343090-dsjq98ks.txt
txt: txt/cord-343090-dsjq98ks.txt
summary:
  As with treatment trials, many prevention trials do not 327 report the study phase (n=4, 25%). Most studies were randomised (n=10, 63%) with a parallel Figure 5 shows 341 the total number of planned inclusions and the number of clinical trials for the ten most 342 frequently studied treatments, with hydroxychloroquine being the treatment associated with A clinical primary outcome was defined in 128 out of 198 therapeutic trials (65% ; Table 3) .


id: cord-329350-qrxl5o1e
author: Pan, Angelo
date: 2020-06-09
extension: .txt
mime: text/plain
words: 1664
sentence: 80
flesch: 51
cache: cache/cord-329350-qrxl5o1e.txt
txt: txt/cord-329350-qrxl5o1e.txt
title:
  Suggestions from Cremona, Italy - two months into the pandemic at the frontline of COVID-19 in Europe

summary:
  Early intubation is recommended to manage COVID-19 patients (7) and very rapidly you may run out ventilators. On the HCWs' side, working with COVID-19 patients is an incredible stressful duty since it is a highly transmittable disease.


id: cord-324148-bllyruh8
author: Loubet, Paul
date: 2020-04-10
extension: .txt
mime: text/plain
words: 1553
sentence: 69
flesch: 40
cache: cache/cord-324148-bllyruh8.txt
txt: txt/cord-324148-bllyruh8.txt
title:
  Characteristics of human metapneumovirus infection in adults hospitalized for community-acquired influenza-like illness in France, 2012-2018: a retrospective observational study

summary:
  This was a retrospective, observational, multicenter cohort study using prospectively collected data from adult patients hospitalized during influenza virus circulation, for at least 24h, for community-acquired ILI (with symptom onset <7 days). In our post-hoc analysis of 3148 hospitalized adult patients with community-acquired ILI, 211 hMPV was found in 3% of the samples.


id: cord-286544-ipmcqz8n
author: Cheng, Biao
title: Predictors of progression from moderate to severe COVID-19: a retrospective cohort
date: 2020-07-02
extension: .txt
mime: text/plain
words: 1984
sentence: 92
flesch: 48
cache: cache/cord-286544-ipmcqz8n.txt
txt: txt/cord-286544-ipmcqz8n.txt
summary:
  CONCLUSIONS: Higher levels of NLR and CRP at admission were associated with poor prognosis of moderate COVID-19 patients. However, randomized controlled trials (RCTs) are required to confirm the impact of drug treatment on moderate COVID-19 patients.


id: cord-307213-i8yijbiu
author: Ip, Jonathan Daniel
date: 2020-11-02
extension: .txt
mime: text/plain
words: 1047
sentence: 36
flesch: 42
cache: cache/cord-307213-i8yijbiu.txt
txt: txt/cord-307213-i8yijbiu.txt
title:
  Intrahost non-synonymous diversity at a neutralising antibody epitope of SARS-CoV-2 spike protein N-terminal domain

summary:
  This study aims to determine viral genome diversity in serial samples of COVID-19 patients. The frequency of G22017T increased from ≤5% (nanopore: 3.8%; Illumina: 5%) from first respiratory tract specimen (sputum) to ≥60% (nanopore: 67.7%; Illumina: 60.4%) in the second specimen (saliva; collected 2 days after the 1(st) specimen).


id: cord-351028-p5cq2is5
author: Yang, Jia-Wei
title: Corticosteroid administration for viral pneumonia: COVID-19 and beyond
date: 2020-06-27
extension: .txt
mime: text/plain
words: 1062
sentence: 40
flesch: 26
cache: cache/cord-351028-p5cq2is5.txt
txt: txt/cord-351028-p5cq2is5.txt
summary:
  Observational studies showed that corticosteroid treatment was associated with increased mortality and nosocomial infections for influenza and delay virus clearance for SARS-CoV and MERS-CoV. Limited data on corticosteroid therapy for COVID-19 were reported. Compared with non-severe patients, severe patients were more likely to receive corticosteroid therapy (201/382, 52.6% vs 201/1310, 15.3%).


id: cord-291272-srt08jh8
author: Peters, E.J.G.
date: 2020-10-14
extension: .txt
mime: text/plain
words: 2325
sentence: 86
flesch: 42
cache: cache/cord-291272-srt08jh8.txt
txt: txt/cord-291272-srt08jh8.txt
title:
  Outcomes of persons with COVID-19 in hospitals with and without standard treatment with (Hydroxy)chloroquine

summary:
  We performed a 186 subgroup analysis in (H)CQ hospitals that started (H)CQ directly from the moment of diagnosis versus 187 outcomes in non-(H)CQ hospitals. Primary outcome was 21-day all-cause mortality, defined as hospital mortality, 168 or discharge to a hospice care facility.


id: cord-326703-akn92p1r
author: Bartoletti, Michele
date: 2020-08-08
extension: .txt
mime: text/plain
words: 2210
sentence: 104
flesch: 48
cache: cache/cord-326703-akn92p1r.txt
txt: txt/cord-326703-akn92p1r.txt
title:
  Development and validation of a prediction model for severe respiratory failure in hospitalized patients with SARS-Cov-2 infection: a multicenter cohort study (PREDI-CO study)

summary:
  319 To conclude, we developed and validated an individual risk score including eight strong predictors 320 of SRF to identify at hospital admission patients with COVID-19 diagnosis deserving a high level of 321 care and a prompt medical treatment. mg/dl, and LDH ≥350 IU/L. Our model and risk score performed 281 similarly even in different cohorts, as defined by different hospitals, providing independent 282 validation.


id: cord-297625-eby014gm
author: L'Huillier, A.G.
title: Survival of rhinoviruses on human fingers
date: 2014-12-11
extension: .txt
mime: text/plain
words: 2640
sentence: 102
flesch: 42
cache: cache/cord-297625-eby014gm.txt
txt: txt/cord-297625-eby014gm.txt
summary:
  Infections within families of employees during two fall peaks of respiratory illness Transmission of experimental rhinovirus infection by contaminated surfaces Rhinovirus transmission: one if by air, two if by hand An investigation of the possible transmission of rhinovirus colds through indirect contact Survival of human rhinovirus type 14 dried onto nonporous inanimate surfaces: effect of relative humidity and suspending medium Near disappearance of rhinovirus along a fomite transmission chain Role of infectious secretions in the transmission of rhinovirus Quantitative rhinovirus shedding patterns in volunteers Survival of influenza virus on human fingers An RNA replication-center assay for high content image-based quantifications of human rhinovirus and coxsackievirus infections Potential role of hands in the spread of respiratory viral infections: studies with human parainfluenza virus 3 and rhinovirus 14 Interruption of experimental rhinovirus transmission Efficacy of organic acids in hand cleansers for prevention of rhinovirus infections We thank all volunteers who participated in the experiments as well as Rosemary Sudan for editorial assistance. As rhinovirus transmission depends on the concentration of virus in secretions [4] , this supports expert opinion that aerosol or oral transmission is a rare event


id: cord-294546-0otd1heg
author: Prendki, V.
date: 2019-01-12
extension: .txt
mime: text/plain
words: 3023
sentence: 144
flesch: 36
cache: cache/cord-294546-0otd1heg.txt
txt: txt/cord-294546-0otd1heg.txt
title:
  Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study

summary:
  Infectious Diseases Society of America/American Thoracic Society consensus guidelines on the management of community-acquired pneumonia in adults BTS guidelines for the management of community acquired pneumonia in adults: update Guidelines for the management of adult lower respiratory tract infectionsdfull version Evolving understanding of the causes of pneumonia in adults, with special attention to the role of Pneumococcus Impact of microbiological samples in the hospital management of community-acquired, nursing home-acquired and hospital-acquired pneumonia in older patients Comprehensive molecular testing for respiratory pathogens in community-acquired pneumonia Impact of rapid detection of viral and atypical bacterial pathogens by real-time polymerase chain reaction for patients with lower respiratory tract infection Routine molecular point-of-care testing for respiratory viruses in adults presenting to hospital with acute respiratory illness (ResPOC): a pragmatic, open-label, randomised controlled trial A comparison of nasopharyngeal and oropharyngeal swabbing for the detection of influenza virus by real-time PCR Low-dose computed tomography for the diagnosis of pneumonia in elderly patients: a prospective, interventional cohort study Diagnosis and management of community and hospital acquired pneumonia in adults: summary of NICE guidance Pneumonia in the very old Lower respiratory tract virus findings in mechanically ventilated patients with severe community-acquired pneumonia Viral infection in patients with severe pneumonia requiring intensive care unit admission Viruses detected by systematic multiplex polymerase chain reaction in adults with suspected community-acquired pneumonia attending emergency departments in France Viral pneumonia in older adults Respiratory syncytial virus and other respiratory viral infections in older adults with moderate to severe influenza-like illness Human metapneumovirus: review of an important respiratory pathogen Radiographic and CT features of viral pneumonia CT findings in viral lower respiratory tract infections caused by parainfluenza virus, influenza virus and respiratory syncytial virus Rhinovirusdnot just the common cold Community-acquired pneumonia requiring hospitalization among US adults Heterogeneous and dynamic prevalence of asymptomatic influenza virus infections Respiratory syncytial virus evaluation among asymptomatic and symptomatic subjects in a university hospital in Sao Paulo, Brazil in the period of Viral shedding and transmission potential of asymptomatic and paucisymptomatic influenza virus infections in the community The impact of the 13-valent pneumococcal conjugate vaccine on pneumococcal carriage in the Community Acquired Pneumonia Immunization Trial in Adults (CAPiTA) Study Early chest computed tomography scan to assist diagnosis and guide treatment decision for suspected community-acquired pneumonia key: cord-294546-0otd1heg authors: Prendki, V.; Huttner, B.; Marti, C.; Mamin, A.; Fubini, P.E.; Meynet, M.P.; Scheffler, M.; Montet, X.; Janssens, J.P.; Reny, J.L.; Kaiser, L.; Garin, N.; Stirnemann, J. title: Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study date: 2019-01-12 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2018.12.037 sha: doc_id: 294546 cord_uid: 0otd1heg OBJECTIVES:


id: cord-276399-omjfyog0
author: To, K.K.W.
date: 2019-04-18
extension: .txt
mime: text/plain
words: 3123
sentence: 142
flesch: 39
cache: cache/cord-276399-omjfyog0.txt
txt: txt/cord-276399-omjfyog0.txt
title:
  Respiratory virus infection among hospitalized adult patients with or without clinically apparent respiratory infection: a prospective cohort study

summary:
  To, K.K.W.; Chan, K.-H.; Ho, J.; Pang, P.K.P.; Ho, D.T.Y.; Chang, A.C.H.; Seng, C.W.; Yip, C.C.Y.; Cheng, V.C.C.; Hung, I.F.N.; Yuen, K.-Y. title: Respiratory virus infection among hospitalized adult patients with or without clinically apparent respiratory infection: a prospective cohort study date: 2019-04-18 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2019.04.012 sha: doc_id: 276399 cord_uid: omjfyog0 OBJECTIVES: To determine the viral epidemiology and clinical characteristics of patients with and without clinically apparent respiratory tract infection. Accurate data on the burden of respiratory virus infection is critical for patient management, infection control measures and public health policies.


id: cord-278807-p1crrb8n
author: Antón, A.
date: 2016-03-02
extension: .txt
mime: text/plain
words: 3104
sentence: 120
flesch: 36
cache: cache/cord-278807-p1crrb8n.txt
txt: txt/cord-278807-p1crrb8n.txt
title:
  Virological surveillance of influenza and other respiratory viruses during six consecutive seasons from 2006 to 2012 in Catalonia, Spain

summary:
  Phylogenetic and molecular characterizations of viral haemagglutinin, partial neuraminidase and matrix 2 proteins were performed from a representative sampling of influenza viruses. During these six consecutive seasons other RV than influenza viruses were mainly detected during the cold months, often just before and after the seasonal influenza epidemics ( Fig. 2) , with scarce circulation during the inter-seasonal periods.


id: cord-276212-ys5njiw0
author: Wei, L.
date: 2015-05-30
extension: .txt
mime: text/plain
words: 2862
sentence: 94
flesch: 34
cache: cache/cord-276212-ys5njiw0.txt
txt: txt/cord-276212-ys5njiw0.txt
title:
  Burden, seasonal pattern and symptomatology of acute respiratory illnesses with different viral aetiologies in children presenting at outpatient clinics in Hong Kong

summary:
  Although it is difficult to differentiate between different respiratory viral infections on the basis of clinical symptomatology alone, our results suggested that a number of symptoms were more commonly reported by patients with influenza virus infections than by patients with infections caused by other respiratory viruses. Symptomatology was examined by comparing clinical symptoms of different respiratory virus infections by the use of Pearson's chi-square test (χ 2 ) or Fisher's exact test (FE).


id: cord-293542-o0zspgrk
author: Ippolito, G.
title: Facing the threat of highly infectious diseases in Europe: the need for a networking approach
date: 2014-12-12
extension: .txt
mime: text/plain
words: 2642
sentence: 83
flesch: 34
cache: cache/cord-293542-o0zspgrk.txt
txt: txt/cord-293542-o0zspgrk.txt
summary:
  Research on emerging infectious diseases has been funded since the inception of the European Union (EU) Framework Programmes (FP) for Research in 1985. In total, both influenza research and research on other emerging infectious diseases have received more than €100 million of EU funding each since 2002.


id: cord-326341-egtnqlov
author: Liotti, Flora Marzia
date: 2020-09-23
extension: .txt
mime: text/plain
words: 517
sentence: 18
flesch: 46
cache: cache/cord-326341-egtnqlov.txt
txt: txt/cord-326341-egtnqlov.txt
title:
  Performance of a novel diagnostic assay for rapid SARS-CoV-2 antigen detection in nasopharynx samples

summary:
  Laboratory testing for coronavirus disease (COVID-19) in laboratory-2020.5-eng Evaluation of a rapid diagnostic assay for detection of SARS-CoV-102 2 antigen in nasopharyngeal swabs Evaluation of rapid 104 antigen test for detection of SARS-CoV-2 virus First case of 106 2019 novel coronavirus in the United States Here, we evaluated the performance of the STANDARD F COVID-19 Ag FIA (SD Biosensor, 32 Suwon, South Korea) assay, a fluorescent immunoassay detecting SARS-CoV-2 nucleoprotein 33 antigen, on nasopharynx swab samples.


id: cord-318021-4qrf5m8s
author: Wolfensberger, A.
date: 2019-03-25
extension: .txt
mime: text/plain
words: 3616
sentence: 156
flesch: 37
cache: cache/cord-318021-4qrf5m8s.txt
txt: txt/cord-318021-4qrf5m8s.txt
title:
  Development and validation of a semi-automated surveillance system—lowering the fruit for non-ventilator-associated hospital-acquired pneumonia (nvHAP) prevention()

summary:
  This would translate to a calculated workload for nvHAP surveillance in our 950-bed tertiary care centre of approximately 40 min per workday when using the semiautomatic surveillance system. This approach significantly reduces manual surveillance workload, thus making continuous nvHAP surveillance feasible as a pivotal element for successful prevention efforts.


id: cord-333334-90q1xkld
author: Shengchen, D.
date: 2019-06-20
extension: .txt
mime: text/plain
words: 3882
sentence: 158
flesch: 34
cache: cache/cord-333334-90q1xkld.txt
txt: txt/cord-333334-90q1xkld.txt
title:
  Evaluation of a molecular point-of-care testing for viral and atypical pathogens on intravenous antibiotic duration in hospitalized adults with lower respiratory tract infection: a randomized clinical trial

summary:
  Considering that length of hospital stay for LRTI patients was directly related to duration of intravenous antibiotics, we finally chose duration of intravenous antibiotics as the primary outcome. In our study adding POCT to routine real-time PCR testing shortened the duration of intravenous antibiotic treatment, reduced the length of stay and cost of hospitalization, and improved early de-escalation of intravenous antibiotics compared with routine real-time PCR assays in hospitalized LRTI patients.


id: cord-252569-9rv1p3qh
author: Zanella, M.-C.
date: 2019-01-11
extension: .txt
mime: text/plain
words: 4175
sentence: 166
flesch: 29
cache: cache/cord-252569-9rv1p3qh.txt
txt: txt/cord-252569-9rv1p3qh.txt
title:
  High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis. A narrative review and clinical appraisal

summary:
  Beyond viruses: clinical profiles and etiologies associated with encephalitis Infectious encephalitis in France in 2007: a national prospective study Causes of encephalitis and differences in their clinical presentations in England: a multicentre, population-based prospective study Acute bacterial and viral meningitis Viral infections of the central nervous system in Spain: a prospective study Viral meningitis Etiology of aseptic meningitis and encephalitis in an adult population Guidelines on the management of infectious encephalitis in adults Genetic characterization of human herpesvirus type 1: full-length genome sequence of strain obtained from an encephalitis case from India Analysis of an echovirus 18 outbreak in Thuringia, Germany: insights into the molecular epidemiology and evolution of several enterovirus species B members Late Ebola virus relapse causing meningoencephalitis: a case report Toscana virus genome stability: data from a meningoencephalitis case in Mantua Phylogenetic and epidemiologic evidence of multiyear incubation in human rabies Metagenomic and metabolomic characterization of rabies encephalitis: new insights into the treatment of an ancient disease Isolation of Toscana virus from the cerebrospinal fluid of a man with meningitis in Marseille Toscana virus meningitis case in Switzerland: an example of the ezVIR bioinformatics pipeline utility for the identification of emerging viruses A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012-14): a retrospective cohort study Afebrile meningoencephalitis with transient central facial paralysis due to Toscana virus infection, southeastern France Molecular epidemiology of human enterovirus 71 at the origin of an epidemic of fatal hand, foot and mouth disease cases in Cambodia A variegated Squirrel Bornavirus associated with fatal human encephalitis Isolation and complete genome analysis of neurotropic dengue virus serotype 3 from the cerebrospinal fluid of an encephalitis patient Astrovirus MLB2, a new gastroenteric virus associated with meningitis and disseminated infection Nextgeneration sequencing for diagnosis and tailored therapy: a case report of astrovirus-associated progressive encephalitis Acute encephalopathy in an immunocompromised boy with astrovirus-MLB1 infection detected by next generation sequencing Human coronavirus OC43 associated with fatal encephalitis A new arenavirus in a cluster of fatal transplant-associated diseases Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage Identification of a new cyclovirus in cerebrospinal fluid of patients with acute central nervous system infections A cluster of fatal tick-borne encephalitis virus infection in organ transplant setting A novel cause of chronic viral meningoencephalitis: Cache Valley virus Astrovirus VA1/HMO-C: an increasingly recognized neurotropic pathogen in immunocompromised patients Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing Diagnosis of neuroinvasive astrovirus infection in an immunocompromised adult with encephalitis by unbiased next-generation sequencing Deep sequencing to identify the causes of viral encephalitis Next-generation sequencing (NGS) in the identification of encephalitiscausing viruses: unexpected detection of human herpesvirus 1 while searching for RNA pathogens Detection of virus in CSF from the cases with meningoencephalitis by next-generation sequencing A new densovirus in cerebrospinal fluid from a case of anti-NMDA-receptor encephalitis Suspected encephalitis with Candida tropicalis and Fusarium detected by unbiased RNA sequencing Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system Acute West Nile virus meningoencephalitis diagnosed via metagenomic deep sequencing of cerebrospinal fluid in a renal transplant patient Deep sequencing reveals persistence of cell-associated mumps vaccine virus in chronic encephalitis Diagnosis of fatal human case of St. Louis encephalitis virus infection by metagenomic sequencing An emerging opportunistic infection: fatal astrovirus (VA1/HMO-C) encephalitis in a pediatric stem cell transplant recipient Actionable diagnosis of neuroleptospirosis by next-generation sequencing Diagnosing Balamuthia mandrillaris encephalitis with metagenomic deep sequencing Human parvovirus 4 as potential cause of encephalitis in children Astrovirus encephalitis in boy with X-linked agammaglobulinemia Identification of viruses in cases of pediatric acute encephalitis and encephalopathy using next-generation sequencing Detection of Toscana virus from an adult traveler returning to Australia with encephalitis Neurobrucellosis: unexpected answer from metagenomic nextgeneration sequencing Human anelloviruses: an update of molecular, epidemiological and clinical aspects Human anelloviruses and the central nervous system Low prevalence of TT virus in the cerebrospinal fluid of viremic patients with central nervous system disorders TT virus has a ubiquitous diffusion in human body tissues: analyses of paired serum and tissue samples Deep sequencing for the detection of virus-like sequences in the brains of patients with multiple sclerosis: detection of GBV-C in human brain Detection of GB virus C genomic sequence in the cerebrospinal fluid of a HIV-infected patient in China: a case report and literature review Human pegivirus-1 in the CSF of patients with HIVassociated neurocognitive disorder (HAND) may be derived from blood in highly viraemic patients The management of encephalitis: clinical practice guidelines by the Infectious Diseases Society of America The changing face of pathogen discovery and surveillance Validation of metagenomic next-generation sequencing tests for universal pathogen detection key: cord-252569-9rv1p3qh authors: Zanella, M.-C.; Lenggenhager, L.; Schrenzel, J.; Cordey, S.; Kaiser, L. title: High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis.


id: cord-287256-hgqz1bcs
author: Magurano, Fabio
date: 2020-11-05
extension: .txt
mime: text/plain
words: 1180
sentence: 44
flesch: 48
cache: cache/cord-287256-hgqz1bcs.txt
txt: txt/cord-287256-hgqz1bcs.txt
title:
  SARS-CoV-2 infection: the environmental endurance of the virus can be influenced by the increase of temperature

summary:
  Viral titre of the daily collections of 0, 24, 48 and 72 hours at RT were determined also by plaque assay in Vero E6 cells. Several studies have shown that viral spread could be influenced by climatic conditions since enveloped viruses tend to reduce their circulation in summertime due to high temperature and solar radiation (2, 3) .


id: cord-344581-h7ikjgic
author: Ong, David S.Y.
date: 2020-06-02
extension: .txt
mime: text/plain
words: 2076
sentence: 83
flesch: 47
cache: cache/cord-344581-h7ikjgic.txt
txt: txt/cord-344581-h7ikjgic.txt
title:
  Comparison of diagnostic accuracies of rapid serological tests and ELISA to molecular diagnostics in patients with suspected COVID-19 presenting to the hospital

summary:
  Clinical Characteristics of Coronavirus Disease 2019 in China Rapidly increasing cumulative incidence of coronavirus disease (COVID-19) in the European Union/European Economic Area and the United Kingdom Current information about the novel coronavirus (COVID-19) Bilthoven: RIVM Better tests, better care: improved diagnostics for infectious diseases SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR Performance of VivaDiag COVID-19 IgM/IgG Rapid Test is inadequate for diagnosis of COVID-19 in acute patients referring to emergency room department Evaluation of a COVID-19 IgM and IgG rapid test; an efficient tool for assessment of past exposure to SARS-CoV-2 Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease Antibody Detection and Dynamic Characteristics in Patients with COVID-19 Boson Biotech Rapid 2019-nCoV IgG/IgM Combo Test Card 10 / 20 (50% Cellex qSARS-CoV-2 IgG/IgM Cassette Dynamiker Biotechnology 2019-nCOV IgG/IgM Orient Gene Biotech COVID-19 IgG/IgM Rapid Test Cassette 11 / 20 (55% Prometheus Bio 2019-nCOV IgG/IgM In the subgroup of patients with time from symptom onset to sample collection >= 14 days, sensitivity and specificity of the LFA were 9/14 (64%; 95%CI 39-89) and 30/32 (94%; 95%CI 85-100), respectively, whereas sensitivity and specificity of the ELISA Of note, sensitivity was 17/24 (71%) in patients with >=7 days from symptom onset to sample collection and CRP >=100 mg/L We would like to thank our laboratory technicians and team managers for their assistance in performing the serological tests. This study aimed to assess the diagnostic performance of LFAs, and compare these to an enzyme-linked immunosorbent assay (ELISA) and NATs in suspected COVID-19 patients.


id: cord-300023-2dg7njki
author: Pillet, S.
title: Contamination of healthcare workers' mobile phones by epidemic viruses()
date: 2015-12-20
extension: .txt
mime: text/plain
words: 3087
sentence: 129
flesch: 46
cache: cache/cord-300023-2dg7njki.txt
txt: txt/cord-300023-2dg7njki.txt
summary:
  We aimed to evaluate the presence of virus RNA from epidemic viruses including metapneumovirus, respiratory syncytial virus, influenza viruses, rotavirus (RV) and norovirus on the MPs used by healthcare workers (HCWs) and to relate it to hygiene measures. The presence of virus RNA was significantly associated with MPs from the paediatric HCWs (p <0.001).


id: cord-325529-pid58g2r
author: Ben-Ami, Roni
title: Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection
date: 2020-06-23
extension: .txt
mime: text/plain
words: 2830
sentence: 122
flesch: 45
cache: cache/cord-325529-pid58g2r.txt
txt: txt/cord-325529-pid58g2r.txt
summary:
  Here we describe and demonstrate practical pooling solutions that save time and reagents by performing RNA extraction and RT-PCR on pooled samples. Alternatively, it is possible to dynamically adapt pooling sizes, when the measured rate of positive samples is different than expected.


id: cord-023592-w96h4rir
title: Abstracts cont.
date: 2015-12-28
extension: .txt
mime: text/plain
words: 67976
sentence: 3236
flesch: 48
cache: cache/cord-023592-w96h4rir.txt
txt: txt/cord-023592-w96h4rir.txt
summary:
  The maximum amino acid identities of genes among different non-antibiotic-producing bacterial isolates were close to 100% for most genes, but those between antibiotic-producing and human or animal bacteria ranged from <28 to <77%. Results: Seven or eight participants provided qualifying results in the two separate QC studies, and the calculated (proposed) ranges were (range; % results in range): E. faecalis ATCC 29212 (2-8 mg/ L; 95.6), S. aureus ATCC 29213 (0.5-2 mg/L; 99.4), S. pneumoniae ATCC 49619 (0.25-1 mg/L; 97.5 and 30-37 mm; 97.6), H. influenzae ATCC 49247 (1-4 mg/L; 97.5 and 24-32 mm; 99.8), and S. aureus ATCC 25923


id: cord-009664-kb9fnbgy
title: Oral presentations
date: 2014-12-24
extension: .txt
mime: text/plain
words: 71226
sentence: 3280
flesch: 44
cache: cache/cord-009664-kb9fnbgy.txt
txt: txt/cord-009664-kb9fnbgy.txt
summary:
  Resistance to penicillin, clindamycin and tetracycline fluctuated over time at~75%, 4−8% and 2−10% respectively. The median expected power was 10.0% (IQR, 7.2−13.6%) for a risk ratio for mortality of 0.85 between the compared groups; 14.7% (IQR, 10.6−21.8%) for a risk ratio of 0.80; and 7.9% (IQR, 6.3−10.2%) for a reduction in mortality from 30% to 25%.


id: cord-019490-m1cuuehi
title: Abstracts cont.
date: 2015-12-28
extension: .txt
mime: text/plain
words: 93719
sentence: 4340
flesch: 45
cache: cache/cord-019490-m1cuuehi.txt
txt: txt/cord-019490-m1cuuehi.txt
summary:
  Mean age (78 vs 77), Charlson score (2.5 vs. 2.6), neoplasm (22% vs. 21%), HIV (0.7% vs. 0.8%), chronic liver disease (9% vs.7%), diabetes mellitus ( 19% vs.22%), ICU admission (4% vs. 4%), monotherapy (63% vs. 66%), and aetiology (S. pneumoniae 34% vs. 36%; L. pneumophila 3% vs.2%; others 8% vs.11%; unknown 54% vs.51%) were similar. The same was found for mecillinam, i.e. no correlation for AUC/MIC vs. CFÚ s in urine or organs, while Time > MIC % significantly (P < 0.05) correlated with CFÚ s in urine (R 2 = 0.48), and kidney tissue (R 2 = 0.82), respectively.


id: cord-022501-9wnmdvg5
title: P1460 – P1884
date: 2015-12-28
extension: .txt
mime: text/plain
words: 128422
sentence: 6046
flesch: 46
cache: cache/cord-022501-9wnmdvg5.txt
txt: txt/cord-022501-9wnmdvg5.txt
summary:
  In the first half-year of 2005 family doctors most often prescribed penicyllins -(44.8%), makrolids -(27.1%), cephalosporins -(12.5%), tetracyclins -(9.4%) and lincozamidsbased (3.1%) treatments Specialist doctors, on the other hand, prescribed penicllins (41.7%), makrolids (17.9%), cephalosporins (17.7%), tetracyclins (12.1%), lincozamids (5.2%) and chinolons (3%). State-wide antibiotic consumption in the AC setting during the same time was 12 DID (~85% of total consumption).


# url

id: cord-291729-4l4v9jxd
domain: www.fda.gov
url:
  https://www.fda.gov/newsevents/press-announcements/coronavirus-covid-19-update-fda-issues-first-emergencyauthorization-sample-pooling-diagnostic)


# pos

id: cord-291729-4l4v9jxd
sid: 86
tid: 14
pos: ADJ
token:
  https://www.fda.gov/newsevents/press-announcements/coronavirus-covid-19-update-fda-issues-first-emergencyauthorization-sample-pooling-diagnostic

lemma:
  https://www.fda.gov/newsevents/press-announcements/coronavirus-covid-19-update-fda-issues-first-emergencyauthorization-sample-pooling-diagnostic


